BRPI1008532B1 - ISOLATED PROTEIN FRAMEWORK, METHOD FOR BUILDING AN ISOLATED PROTEIN FRAMEWORK LIBRARY, ISOLATED NUCLEIC ACID MOLECULE, ISOLATED NUCLEIC ACID VECTOR, BACTERIAL OR FUNGUS HOST CELL, COMPOSITION, MEDICAL DEVICE AND MANUFACTURING ARTICLE FOR PRODUCT USE IN HUMAN BEINGS - Google Patents

Abstract

COMPOSITIONS, METHODS AND USES FOR FRAMEWORK BASED ON THE FIBRONECTIN TYPE III DOMAIN. The present invention relates to a protein scaffold based on a consensus sequence of a tenth repeat of fibronectin type III (FN3) obtained from human fibronectin, including isolated nucleic acids encoding a protein scaffold, vectors, host cells, and methods of making and using the same having applications in therapeutic or diagnostic devices, methods and compositions. In particular, protein scaffold molecules linked to IgG based on the consensus sequence have been identified as useful for therapeutic or diagnostic applications.

Description

FIELD OF THE INVENTION

[0001] The present invention relates to a protein scaffold with novel properties, including the ability to bind to cellular targets. More particularly, the present invention relates to a protein scaffold based on a consensus sequence of a fibronectin type III repeat (FN3).

BACKGROUND OF THE INVENTION

[0002] Monoclonal antibodies are the most widely used class of therapeutic proteins when high affinity and specificity for a target molecule are desired. However, non-antibody proteins that can be engineered to bind to these targets are also of high interest in the biopharmaceutical industry. These "alternative scaffold" proteins may have advantages over traditional antibodies due to their small size, lack of disulfide bonds, high stability, and ability to be expressed in prokaryotic hosts. New purification methods are easily applied; they are easily conjugated to drugs/toxins, effectively penetrate tissues, and are readily formatted into multispecific ligands (Skerra 2000; Binz and Pluckthun 2005).

[0003] One such alternative framework is the immunoglobulin (Ig) fold. This fold is found in the variable regions of antibodies, as well as thousands of non-antibody proteins. It has been shown that such an Ig protein, the tenth repeat of fibronectin type III (FN3) obtained from human fibronectin, can tolerate numerous mutations in surface exposed loops while retaining the overall structure of the Ig fold. In this way, libraries of amino acid variants were constructed on these loops and specific ligands were selected for numerous different targets (Koide et al. 1998; Karatan et al. 2004). Such engineered FN3 domains have been observed to bind to targets with high affinity, while retaining important biophysical properties (Parker et al. 2005).

[0004] Desirable physical properties of potential alternative scaffold molecules include high thermal stability and reversibility of thermal folding and unfolding. Several methods have been applied to increase the apparent thermal stability of proteins and enzymes, including rational design based on comparison to highly similar thermostable sequences, design of stabilizing disulfide bonds, mutations to increase a-helix propensity, manipulation of salt bridges, alteration of protein surface charge, directed evolution, and consensus sequence composition (Lehmann and Wyss 2001). High thermal stability is a desired property of these scaffolds, as it can increase the yield of the obtained recombinant protein, optimize the solubility of the purified molecule, optimize the activity of intracellular scaffolds, decrease immunogenicity, and minimize the need for a cold chain in manufacturing. .

SUMMARY OF THE INVENTION

[0005] The present invention provides a protein framework based on a fibronectin type III repeat protein (FN3), coding or complementary nucleic acids, vectors, host cells, compositions, combinations, formulations, devices and methods for manufacturing and using the same . In a preferred embodiment, the protein framework is composed of a consensus sequence of multiple human fibronectin FN3 domains. In another preferred embodiment, the protein scaffold of the present invention is a consensus sequence of 7 FN3 domains. Protein scaffolds of the invention can be designed to bind various molecules, for example a cellular target protein.

[0006] The protein scaffolds of the invention may include additional molecules or portions, for example, the Fc region of an antibody, an albumin-binding domain, or other portion that influences half-life. In additional embodiments, the protein scaffolds of the invention may be linked to a nucleic acid molecule that can encode the protein scaffold.

[0007] The present invention also provides at least one method for expressing at least one protein scaffold based on a consensus sequence of multiple FN3 domains, in a host cell, comprising culturing the host cell as described in the present invention under conditions in which at least one protein scaffold is expressed in detectable and/or recoverable amounts.

[0008] The present invention also features at least one composition comprising: (a) a protein scaffold based on a consensus sequence of multiple FN3 domains and/or coding nucleic acid as described in the present invention, and (b) a carrier or suitable and/or pharmaceutically acceptable diluent.

[0009] The present invention further comprises a method of generating libraries of a protein scaffold based on a fibronectin type III repeat (FN3) protein, preferably, a consensus sequence of multiple FN3 domains, and more preferably, a consensus sequence of multiple human fibronectin FN3 domains. The library is formed by producing successive generations of scaffolds, changing (by mutation) the amino acids or the number of amino acids in the molecules, at specific positions in the portions of the scaffold, for example in the loop regions. Libraries can be generated by changing the amino acid composition of a single loop or by changing multiple loops simultaneously. The loops that are changed can be lengthened or shortened as needed. Such libraries can be generated to include, at each position, all possible amino acids or a certain subset of amino acids. Library elements can be used for display screening, such as in vitro display (DNA, RNA, ribosome display) and phage display.

[00010] The protein scaffolds of the present invention offer optimized biophysical properties, such as stability under reducing conditions and solubility at high concentrations, and can be expressed and folded in prokaryotic systems such as E. coli, in eukaryotic systems such as yeast, and in transcription systems / in vitro translation as the rabbit reticulocyte lysate system.

[00011] In a further aspect, the present invention provides a method for generating a scaffold molecule that binds to a particular target by traversing the scaffold library of the invention with targeting and detection ligands. In other related aspects, the invention comprises screening methods that can be used to generate or affinity mature protein scaffolds with the desired activity, for example capable of binding target proteins with a certain affinity. Affinity maturation can be achieved through iterative cycles of mutagenesis and selection, using systems such as phage display or in vitro display. Mutagenesis during this process may be the result of site-directed mutagenesis to specific framework residues, random mutagenesis due to error-prone PCR, DNA scrambling, and/or a combination of these techniques. The present invention additionally features any invention described herein.

DESCRIPTION OF THE FIGURES

[00012] Figure 1. Structure of the FN3 domain. Crystal structure of the 10th FN3 domain of human fibronectin (PDB 1TTF) (Main, et al., Cell 71: 671-8, 1992). The B:C, D:E, and F:G loops that underwent diversification are identified.

[00013] Figures 2A-N. Fusion profiles of purified FN3 domains (with the exception of the 7th domain) of human fibronectin as determined by DSC in PBS pH 7.4.

[00014] Figure 3. Multiple sequence alignment of the 15 FN3 domains of human fibronectin. The alignment was produced using the VectorNTI program.

[00015] Figure 4. Alignment of multiple sequences of FN3 domains 1, 5, 8, 10, 12, 14, and 15 of human fibronectin. The alignment was produced using the VectorNTI program.

[00016] Figures 5A and B. Expression and purification of fibcon. A) A 4-12% SDS-PAGE analysis showing total cell lysate, soluble fraction, Ni-NTA flux, and fractions eluted from the Ni-NTA column. B) Superdex 75 purification of fibcon in PBS. Arrows show elution volume and mass of molecular weight standards.

[00017] Figure 6. Differential scanning calorimetry of fibcon in PBS pH 7.4.

[00018] Figure 7. Gu-HCl-induced unfolding of fibcon monitored by intrinsic tryptophan fluorescence. Excitation was at a wavelength of 280 nm and emission at 365 nm.

[00019] Figure 8. The amino acid sequence of fibcon showing the location of loops A-B, B-C, C-D, D-E, E-F, F-G.

DESCRIPTION OF THE INVENTION

[00020] The present invention features an isolated, recombinant and/or synthetic protein scaffold based on a fibronectin type III repeat (FN3) protein including, without limitation, mammalian-derived scaffold, as well as coding nucleic acid molecules and compositions comprising at least one polynucleotide encoding a protein framework based on the tenth FN3 domain. The present invention further includes, but is not limited to, methods for making and using such nucleic acids and protein scaffolds, including diagnostic and therapeutic compositions, methods, and devices.

[00021] The protein scaffolds of the present invention offer advantages over conventional therapy, such as the ability to administer locally, orally or across the blood-brain barrier, the ability to express in E. Coli, which allows for an increase in protein expression as a function of mammalian cell resources versus expression, the ability to be engineered into bispecific molecules that bind to multiple targets or multiple epitopes of the same target, the ability to conjugate to drugs, polymers and probes, the ability to be formulated into high concentrations, and the ability of these molecules to effectively penetrate diseased tissues and tumors.

[00022] Furthermore, protein scaffolds exhibit many of the properties of antibodies with respect to their folding, which mimics the variable region of an antibody. This orientation allows the FN3 loops to be exposed similarly to the antibody complementarity determining regions (CDRs). They need to be able to bind to cellular targets, and the bonds can be altered, for example affinity matured, to optimize certain binding or related properties.

[00023] Three of the six loops of the protein backbone of the invention correspond topologically to the complementarity determining regions (CDRs 1 to 3), i.e. the antigen-binding regions of an antibody, while the remaining three loops are exposed on the surface similar to antibody CDRs. These loops span residues 13-16, 22-28, 38-43, 51-54, 60-64, and 75-81 of SEQ. ID No. 16, as shown in Table 3, below, and in Figure 8. Preferably, the loop regions at residues 22-28, 51-54, and 75-81 are altered for specificity and binding affinity. These loop regions are randomized to populate a library and potent binders can be selected from the library that have high affinity for a particular protein target. One or more of the loop regions may interact with a target protein, similar to an antibody CDR interaction with the protein.

[00024] The scaffolds of the present invention may incorporate other subunits, for example via covalent interaction. All or a portion of an antibody constant region can be linked to the scaffold to impart properties similar to those of an antibody, for example complement activity (ADCC), half-life, etc. For example, effector function can be provided and/or controlled, for example by modifying C1q binding and/or FCYR binding and thereby altering CDC and/or ADCC activity. "Effector functions" are responsible for activating or decreasing a biological activity (eg, in an individual). Examples of effector functions include, but are not limited to: C1q binding, complement-dependent cytotoxicity (CDC), Fc receptor binding, cell-mediated and antibody-dependent cytotoxicity (ADCC), phagocytosis, downregulation of surface receptors cell (e.g. B cell receptor, BCR), etc. These effector functions may require the Fc region to be combined with a binding domain (e.g., protein scaffold loops) and can be evaluated using various tests (e.g., Fc binding tests, ADCC tests, CDC tests, etc.).

[00025] Additionally, molecules of a conjugate of toxins, albumin, albumin ligands or polyethylene glycol (PEG) can be linked to the scaffold molecule to obtain desired properties. Any such fusion can be generated using standard techniques, for example, by expressing the fusion protein from a recombinant fusion gene constructed using publicly available gene sequences.

[00026] The scaffolds of the present invention can be used as monospecific in monomeric form, or as bi or multispecific (for different target proteins or different epitopes on the same target protein) in multimeric form. Bonds can be covalent or non-covalent. For example, a dimeric bispecific scaffold has a subunit with specificity for a first target protein or epitope and a second subunit with specificity for a second target protein or epitope. The scaffold subunits can be joined in a variety of conformations that can increase the valence and therefore the avidity of antigen binding.

[00027] For use in the present invention, an "antibody" includes any protein or peptide-containing molecule that comprises at least a portion of an immunoglobulin molecule including, but not limited to, at least one complementarity determining region (CDR) of a heavy or light chain, or a linker binding portion thereof, a heavy chain or light chain variable region, a heavy chain or light chain constant region, a framework region, or any portion thereof. The antibody optionally further affects a specific ligand including, but not limited to, instances where the antibody modulates, decreases, enhances, antagonizes, agonizes, mitigates, alleviates, blocks, inhibits, abrogates and/or interferes with at least one activity or binding, or with receptor activity or binding, in vitro, in situ and/or in vivo.

[00028] The term "antibody" is further intended to encompass antibodies, digestion fragments, specified portions and variants thereof, including, without limitation, antibody mimicry or comprising portions of antibodies that mimic the structure and/or function of a specified antibody or fragment or portion thereof, including, without limitation, single chain antibodies, single domain antibodies and fragments thereof. Functional fragments include antigen-binding fragments that bind to a specific target. For example, antibody fragments capable of binding to a specific target or portions thereof, including, but not limited to, Fab fragments (e.g., by papain digestion), Fab' (e.g., by pepsin digestion and reduction partial) and F(ab')2 (eg by pepsin digestion), facb (eg by plasmin digestion), pFc' (eg by pepsin or plasmin digestion), Fd (eg by by pepsin digestion, partial reduction and re-aggregation), Fv or scFv (e.g. by molecular biology techniques) are encompassed by the invention (see, e.g., Colligan, Immunology, supra).

[00029] Such fragments may be produced by enzymatic cleavage, synthetic or recombinant techniques, as known in the art and/or as described in the present invention. Antibodies can also be produced in a variety of truncated forms using antibody genes in which one or more stop codons have been introduced upstream of the natural stop site. For example, a combination gene encoding an F(ab')2 heavy chain portion can be designed to include DNA sequences encoding the CH1 domain and/or the hinge region of the heavy chain. The various portions of antibodies can be chemically joined by conventional techniques, or can be prepared as a contiguous protein using genetic engineering techniques.

[00030] A scaffold protein of the present invention can be used to measure or obtain an effect on a cell, tissue, organ or animal (including mammals and humans), to diagnose, monitor, modulate, treat, alleviate, help prevent the incidence of, or reducing symptoms of, at least one disease or condition selected from, but not limited to, at least one of an immunological disorder or disease, cardiovascular disorder or disease, infectious, malignant and/or neurological disorder or disease, or other known or specified related condition.

[00031] Such a method may comprise administering an effective amount of a composition or a pharmaceutical composition comprising at least one scaffold protein to a cell, tissue, organ, animal or patient in need of such modulation, treatment, relief, prevention or reduction in symptoms, effects or mechanisms. The effective amount may comprise from about 0.001 to 500 mg/kg by single (e.g. bolus), multiple or continuous administration, or enough to achieve a serum concentration of 0.01 to 5,000 µg/ml by single, multiple administration. or continuous, or any effective range or value within that range, as performed and determined using known methods, as described in the present invention or known in the relevant arts.

Framework Protein of the Present Invention - Production and Generation

[00032] The at least one scaffold protein of the present invention may optionally be produced by a cell line, a mixed cell line, an immortalized cell or a clonal population of immortalized cells, as is well known in the art. See, for example, Ausubel, et al., editors, Current Protocols in Molecular Biology, John Wiley & Sons, Inc., NY, NY, USA (1987-2001), Sambrook, et al., Molecular Cloning: A Laboratory Manual , 2nd Edition, Cold Spring Harbor, NY, USA (1989), Harlow and Lane, Antibodies, a Laboratory Manual, Cold Spring Harbor, NY, USA (1989), Colligan, et al., editors, Current Protocols in Immunology, John Wiley & Sons, Inc., NY, USA (1994-2001), Colligan et al., Current Protocols in Protein Science, John Wiley & Sons, NY, NY, USA, (1997-2001).

[00033] Amino acids obtained from a scaffold protein can be altered, added and/or deleted to reduce immunogenicity or to reduce, enhance or modify binding, affinity, association rate, dissociation rate, avidity, specificity, half- life, stability, solubility or any other suitable characteristic, as is known in the art.

[00034] Optionally, scaffold proteins can be engineered with retention of high affinity for the antigen and other favorable biological properties. To achieve this goal, scaffold proteins can optionally be prepared through a process of analyzing the parental sequences and various conceptual manipulated products using three-dimensional models of the parental and manipulated sequences. Three-dimensional models are commonly available and familiar to those skilled in the art. Computer programs are available that illustrate and display likely three-dimensional conformational structures of selected candidate sequences, and can measure possible immunogenicity (eg, the Immunofilter program from Xencor, Inc., of Monrovia, CA, USA). Inspection of these displays allows analysis of the likely role played by residues in the functioning of the candidate sequence, that is, analysis of residues that influence the ability of the candidate scaffold protein to bind its antigen. In this way, residues can be selected and combined from the parental and reference sequences so that the desired characteristic, such as affinity for one or more target antigens, is obtained. Alternatively, or in addition to the above procedures, other suitable engineering methods may be used.

screening

[00035] Screening of protein scaffolds for specific binding to similar proteins or fragments can be conveniently accomplished using nucleotide display (DNA or RNA display) or peptide display libraries, for example in vitro display. This method involves screening large collections of peptides for individual members with the desired function or structure. The nucleotide or peptide sequences displayed can be from 3 to 5,000 or more nucleotides or amino acids in length, often from 5 to 100 amino acids, and often from about 8 to 25 amino acids. In addition to direct chemical synthesis methods for generating peptide libraries, several methods with recombinant DNA have been described. One type involves displaying a peptide sequence on the surface of a bacteriophage or cell. Each bacteriophage or cell contains the nucleotide sequence that encodes the specific peptide sequence displayed. These methods are described in PCT Patent Publications Nos. 91/17271, 91/18980, 91/19818 and 93/08278.

[00036] Other systems for generating peptide libraries have aspects of both in vitro chemical synthesis and recombinant methods. See PCT Patent Publications Nos. 92/05258, 92/14843 and 96/19256. See also U.S. Patent Nos. 5,658,754 and 5,643,768. Peptide display libraries, vector and screening kits are commercially available from vendors such as Invitrogen (Carlsbad, CA, USA), and Cambridge Antibody Technologies (Cambridgeshire, UK). See, e.g., U.S. Patents No. 4704692, 4939666, 4946778, 5260203, 5455030, 5518889, 5534621, 5656730, 5763733, 5767260 and 5856456 assigned to Enzon, 5223409, 5403484, 5571698 and 5837500 assigned to Dyax, 5427908 and 5580717 assigned to Affymax, 5885793 assigned to Cambridge Antibody Technologies, 5750373 assigned to Genentech, 5618920, 5595898, 5576195, 5698435, 5693493 and 5698417 assigned to Xoma, Colligan, cited above, Ausubel, cited above, or Sambrook, cited above.

[00037] The protein scaffolds of the invention can bind human or other mammalian proteins with a wide range of affinities (KD). In a preferred embodiment, at least one protein scaffold of the present invention may optionally bind a target protein with a very high degree of affinity, for example with a KD equal to or less than about 10 -7 M , including, but not limited to, 0.1 to 9.9 (or any range or value in that range) X 10-8, 10-9, 10-10, 10-11, 10-12, 10-13 , 10-14, 10-15 or any range or value in that range as determined by surface plasmon resonance or the KinExA method as practiced by those skilled in the art.

[00038] The affinity or avidity of a protein scaffold for an antigen can be determined experimentally using any suitable method. (See, for example, Berzofsky, et al., "Antibody-Antigen Interactions," in Fundamental Immunology, Paul, WE, Ed., Raven Press: New York, NY, USA (1984); Kuby, Janis Immunology, WH Freeman and Company: New York, NY, USA (1992); and methods described herein). The measured affinity of a specific interaction between protein scaffold and antigen may vary if measured under different conditions (eg, salt concentration, pH). Therefore, measurements of affinity and other antigen binding parameters (e.g. KD, Kon, Koff) are preferably done with standardized solutions of protein and antigen scaffold, and with a standardized buffer such as the buffer described here. .

[00039] Competitive assays can be performed with the protein scaffold of the present invention in order to determine which proteins, antibodies and other antagonists compete for binding to a target protein with the protein scaffold of the present invention, and/or share the epitope region. Such assays, as is readily known to those skilled in the art, assess competition between antagonists or ligands for a limited number of binding sites on a protein. The protein and/or antibody is immobilized or rendered insoluble, before or after competition, and the sample bound to the target protein is separated from the unbound sample, for example by decanting (if it has previously become insoluble protein or antibody) or by centrifugation (in cases where the protein or antibody has precipitated after the competitive reaction). Furthermore, competitive binding may be determined by whether the function has been altered by binding or not binding the protein backbone to the target protein, for example, whether the protein backbone molecule inhibits or potentiates the enzymatic activity of, for example a bookmark. ELISA and other functional tests may be used, as is well known in the art.

Nucleic Acid Molecules

[00040] The nucleic acid molecules of the present invention encoding protein scaffolds may be in the form of RNA, such as mRNA, hnRNA, tRNA or any other form, or in the form of DNA including, but not limited to, cDNA and genomic DNA obtained by cloning or produced synthetically, or any combination thereof. DNA can be triple, double or single stranded, or any combination thereof. Any portion of at least one strand of DNA or RNA can be a coding strand, also known as a sense strand, or it can be the non-coding strand, also known as an antisense strand.

[00041] Isolated nucleic acid molecules of the present invention may include nucleic acid molecules comprising an open reading frame (ORF), optionally with one or more introns, for example, but not limited to, at least a specified portion of at least one protein scaffold, nucleic acid molecules comprising the coding sequence for a protein scaffold or loop region that binds to the target protein, and nucleic acid molecules comprising a nucleotide sequence substantially different from those described above but which, due to the degeneracy of the genetic code, still encode the protein framework as described in the present invention and/or as is known in the art. Of course, the genetic code is well known in the art. Therefore, it would be routine for one skilled in the art to generate such degenerate nucleic acid variants that encode the protein scaffolds of the present invention. See, for example, Ausubel, et al., supra, and such nucleic acid variants are included in the present invention.

[00042] As indicated herein, nucleic acid molecules of the present invention that comprise a nucleic acid encoding a protein scaffold may include, but are not limited to, those encoding the amino acid sequence of a protein scaffold fragment by itself , the coding sequence for the entire protein framework or a portion thereof, the coding sequence for a protein framework, a fragment or a portion, as well as additional sequences, such as the coding sequence for at least one leader of signal or fusion peptide, with or without the aforementioned additional coding sequences, such as at least one intron, together with additional non-coding sequences, including, but not limited to, 5' and 3' non-coding sequences, such as the transcribed sequences and untranslated proteins that play a role in transcription, mRNA processing, including splicing and polyadenylation signals (e.g., DNA ligation). and ribosome and mRNA stability), an additional coding sequence that encodes additional amino acids, such as those that provide additional functionality. Therefore, the sequence encoding a protein scaffold may be fused to a marker sequence, such as a sequence encoding a peptide that facilitates purification of the fused protein scaffold comprising a protein scaffold fragment or portion.

Polynucleotides Selectively Hybridizing to a Polynucleotide As Described in the Present Invention

[00043] The present invention provides isolated nucleic acids that hybridize under selective hybridization conditions to a polynucleotide described herein. Therefore, polynucleotides of this embodiment can be used to isolate, detect and/or quantify nucleic acids comprising such polynucleotides. For example, the polynucleotides of the present invention can be used to identify, isolate or amplify partial or full-length clones in a deposited library. In some embodiments, the polynucleotides are genomic or cDNA sequences isolated from, or otherwise complementary to, a cDNA obtained from a human or mammalian nucleic acid library.

[00044] Preferably, the cDNA library comprises at least 80% full-length sequences, preferably at least 85% or 90% full-length sequences, and more preferably at least 95% full-length sequences . cDNA libraries can be normalized to increase representation of rare sequences. Low or moderate stringency hybridization conditions are typically, but not exclusively, employed with sequences that have reduced sequence identity to complementary sequences. Moderate and high stringency conditions can optionally be employed for sequences with higher identity. Low stringency conditions allow selective hybridization of sequences that have about 70% sequence identity and can be employed to identify orthologous or paralogous sequences.

[00045] Optionally, the polynucleotides of the present invention will encode at least a portion of a protein framework encoded by the polynucleotides described herein. The polynucleotides of the present invention encompass nucleic acid sequences that can be used for selective hybridization with a polynucleotide that encodes a protein scaffold of the present invention. See, for example, Ausubel, supra, and Colligan, supra, each of which is incorporated herein by reference in their entirety.

Nucleic acid construction

[00046] The isolated nucleic acids of the present invention may be produced using (a) recombinant methods, (b) synthetic techniques, (c) purification techniques, and/or (d) combinations thereof, as is convenient. known in the art.

[00047] The nucleic acids may conveniently comprise sequences in addition to a polynucleotide of the present invention. For example, a multicloning site that comprises one or more restriction endonuclease sites can be inserted into the nucleic acid to aid in the isolation of the polynucleotide. Furthermore, translatable sequences can be inserted to aid in the isolation of the translated polynucleotide of the present invention. For example, a hexahistidine tag sequence provides a convenient means of purifying the proteins of the present invention. The nucleic acid of the present invention, excluding the coding sequence, is optionally a vector, adapter or linker for cloning and/or expressing a polynucleotide of the present invention.

[00048] Additional sequences may be added to such cloning and/or expression sequences to optimize their function in cloning and/or expression to aid in the isolation of the polynucleotide, or to optimize the introduction of the polynucleotide into a cell. The use of cloning vectors, expression vectors, adapters, and linkers is well known in the art. (See, for example, Ausubel, supra, or Sambrook, supra).

Recombinant Methods for the Construction of Nucleic Acids

[00049] The isolated nucleic acid compositions of this invention, such as RNA, cDNA, genomic DNA or any combination thereof, can be obtained from biological sources using numerous cloning methodologies known to those skilled in the art. In some embodiments, oligonucleotide probes that selectively hybridize, under stringent conditions, to the polynucleotides of the present invention are used to identify the desired sequence in a cDNA or genomic DNA library. RNA isolation and construction of genomic and cDNA libraries are well known to those skilled in the art. (See, for example, Ausubel, supra, or Sambrook, supra).

Nucleic Acid Screening and Isolation Methods

[00050] A genomic and cDNA library can be screened using a probe based on the sequence of a polynucleotide of the present invention, such as those presented herein. The probes can be used to hybridize to genomic DNA or cDNA sequences to isolate homologous genes in the same organism or in different organisms. Those skilled in the art will understand that varying degrees of hybridization stringency can be employed in the test, with either the hybridization or the washing medium being stringent. As the conditions for hybridization become more stringent, there must be a greater degree of complementarity between probe and target for bidirectional formation to occur. The degree of stringency can be controlled by one or more of temperature, ionic strength, pH and the presence of a partially denaturing solvent such as formamide. For example, the stringency of hybridization is conveniently varied by changing the polarity of the reagent solution by, for example, manipulating the concentration of formamide within the range of 0% to 50%. The degree of complementarity (sequence identity) required for detectable binding will vary according to the stringency of the hybridization medium and/or wash medium. The degree of complementarity will optimally be 100%, or 70 to 100%, or any range or value in between. However, it should be understood that minor sequence variations in probes and primers can be compensated for by reducing the stringency of the hybridization and/or wash medium.

[00051] RNA or DNA amplification methods are well known in the art and can be used in accordance with the present invention without undue experimentation, based on the guidelines and teachings presented herein.

[00052] Known methods of amplification of DNA or RNA include, but are not limited to, polymerase chain reaction (PCR) and related amplification processes (see, for example, US Patent Nos. 4,683,195, 4,683. 202, 4,800,159, 4,965,188 assigned to Mullis, et al., 4,795,699 and 4,921,794 assigned to Tabor, et al., 5,142,033 assigned to Innis, 5,122,464 assigned to Wilson, et al. , 5,091,310 assigned to Innis, 5,066,584 assigned to Gyllensten, et al, 4,889,818 assigned to Gelfand, et al, 4,994,370 assigned to Silver, et al, 4,766,067 assigned to Biswas, 4,656,134 assigned to Ringold) and RNA-mediated amplification that uses antisense RNA to the target sequence as a template for the synthesis of double-stranded DNA (US patent 5,130,238 assigned to Malek, et al, under the tradename NASBA), the contents of which are incorporated herein by reference in its entirety. (See, for example, Ausubel, supra, or Sambrook, supra.).

[00053] For example, polymerase chain reaction (PCR) technology can be used to amplify the polynucleotide sequences of the present invention and related genes directly from cDNA or genomic DNA libraries. PCR and other in vitro amplification methods may also be useful, for example, to clone the nucleic acid sequences encoding the proteins to be expressed, to produce nucleic acids, with the aim of using them as probes to detect the presence of desired mRNA in samples, for nucleic acid sequencing, or for other purposes. Examples of techniques sufficient to direct those skilled through in vitro amplification methods are found in Berger, supra, Sambrook, supra, and Ausubel, supra, as well as Mullis, et al., US Patent No. 4,683,202 (1987) , and Innis, et al., PCR Protocols A Guide to Methods and Applications, Eds., Academic Press Inc., San Diego, CA (1990). Commercially available kits for genomic PCR amplification are known in the art. See, for example, Advantage-GC Genomic PCR Kit (Clontech). Additionally, for example, the T4 gene 32 protein (Boehringer Mannheim) can be used to optimize the yield of long PCR products.

Synthetic Methods for Building Nucleic Acids

[00054] The isolated nucleic acids of the present invention can also be prepared by direct chemical synthesis by means of methods (see, for example, Ausubel, et al., above). Chemical synthesis generally produces a single-stranded oligonucleotide, which can be converted to double-stranded DNA through hybridization to a complementarity sequence, or through polymerization with a DNA polymerase using single-stranded DNA as a mold. One skilled in the art will recognize that while DNA synthesis can be limited to sequences of about 100 bases or more, longer sequences can be obtained by ligating shorter sequences.

Recombinant Expression Cassettes

[00055] The present invention further provides recombinant expression cassettes that comprise a nucleic acid of the present invention. A nucleic acid sequence of the present invention, for example a genomic or cDNA sequence encoding a protein scaffold of the present invention, can be used to construct a recombinant expression cassette that can be introduced into at least one desired host cell. A recombinant expression cassette will typically comprise a polynucleotide of the present invention operably linked to transcriptional initiation regulatory sequences that will direct transcription of the polynucleotide in the intended host cell. Heterologous and non-heterologous (i.e., endogenous) promoters can be employed to direct expression of the nucleic acids of the present invention.

[00056] In some embodiments, isolated nucleic acids that function as a promoter, enhancer or other elements may be introduced at the appropriate position (upstream, downstream or in the intron) in a non-heterologous manner of a polynucleotide of the present invention, so to up- or down-regulate the expression of a polynucleotide of the present invention. For example, endogenous promoters can be altered in vivo or in vitro through mutation, deletion and/or substitution.

Vectors and Host Cells

[00057] The present invention also relates to vectors that include the isolated nucleic acid molecules of the present invention, host cells that are genetically engineered with the recombinant vectors, and the production of at least one protein scaffold by means of recombinant techniques, as is well known in the art. See, for example, Sambrook, et al., supra, Ausubel, et al., supra, each of which is incorporated herein by reference in its entirety.

[00058] The polynucleotides may optionally be joined to a vector that contains a selectable marker for propagation in a host. In general, a plasmid vector is introduced into a precipitate, such as a calcium phosphate precipitate, or into a complex with a charged lipid. If the vector is a virus, it can be stored in vitro using a suitable storage cell line and then converted into host cells.

[00059] The DNA insert must be operably linked to a suitable promoter. The expression constructs will also contain sites for initiation of transcription, termination and, in the transcribed region, a ribosomal binding site for translation. The coding portion of the mature transcripts expressed through constructs will preferably include a translation initiation at the beginning and a termination codon (e.g. UAA, UGA or UAG) suitably positioned at the end of the mRNA to be translated, with UAA and UAG are preferred for eukaryotic or mammalian cell expression.

[00060] Expression vectors will preferably include, but optionally, at least one selectable marker. Such labels include, for example, but are not limited to, methotrexate (MTX), dihydrofolate reductase (DHFR, US Pat. 017, resistance to ampicillin, neomycin (G418), mycophenolic acid, or glutamine synthetase (GS, US Pat. in E. coli and other bacteria or prokaryotes (the above patents are fully incorporated herein by reference.) Suitable culture media and conditions for the aforementioned host cells are known in the art. Suitable vectors will be readily apparent to one skilled in the art. Introduction of a vector construct in a host cell can be affected through calcium phosphate transfection, DEAE-dextran mediated transfection, cationic lipid mediated transfection, electroporation, transduction, infection or other known methods. These methods are described in the art, as Sambrook, supra, chapters 1 to 4 and 16 to 18, Ausubel, supra, chapters 1, 9, 13, 15, 16.

[00061] The at least one protein scaffold of the present invention may be expressed in a modified form, as a fusion protein, and may include not only secretion signals, but also additional heterologous functional regions. For example, a region of additional amino acids, particularly charged amino acids, can be added to the amino terminus of a protein scaffold to optimize stability and persistence in the host cell, during purification or during subsequent handling and storage. In addition, peptide moieties can be added to a protein scaffold of the present invention to facilitate purification. These regions can be removed prior to the final preparation of a protein scaffold, or at least a fragment thereof. Such methods are described in many conventional laboratory manuals, such as Sambrook, supra, chapters 17.29 to 17.42 and 18.1 to 18.74, and Ausubel, supra, chapters 16, 17 and 18.

[00062] Those skilled in the art are educated as to the various expression systems available for expressing a nucleic acid encoding a protein of the present invention. Alternatively, the nucleic acids of the present invention may be expressed in a host cell by triggering (by manipulation) a protein scaffold of the present invention in a host cell that contains endogenous DNA encoding. Such methods are well known in the art, for example as described in U.S. Patent Nos. 5,580,734, 5,641,670, 5,733,746 and 5,733,761, incorporated herein by reference in their entirety.

[00063] Illustrative of cell cultures useful for the production of protein scaffolds, specified portions or variants thereof, are bacterial, yeast and mammalian cells, as is known in the art. Mammalian cell systems will often be in the form of single layers of cells, although mammalian cell suspensions or bioreactors may also be used. A number of suitable host cell lines capable of expressing intact glycosylated proteins have been developed in the art, and include the COS-1 cell lines (e.g. ATCC CRL 1650), COS-7 (e.g. ATCC CRL-1651), HEK293, BHK21 (e.g. ATCC CRL-10), CHO (e.g. ATCC CRL 1610) and BSC-1 (e.g. ATCC CRL-26), Cos-7 cells, CHO cells, hep G2 cells, P3X63Ag8. 653, SP2/0-Ag14 cells, 293, HeLa cells and the like, which are readily available, for example, from the American Type Culture Collection of Manassas, VA, USA (www.atcc.org). Preferred host cells include cells of lymphoid origin, such as myeloma and lymphoma cells. Particularly preferred host cells are P3X63Ag8.653 cells (ATCC accession number CRL-1580) and SP2/0-Ag14 cells (ATCC accession number CRL-1851). In a particularly preferred embodiment, the recombinant cell is a P3X63Ab8.653 cell or an SP2/0-Ag14 cell.

[00064] Expression vectors for these cells may include one or more of the following expression control sequences, such as, for example, but not limited to an origin of replication; a promoter (e.g., SV40 late or early promoters, the CMV promoter (US Pat. 1 (US Pat. 5,266,491), at least one human promoter; an enhancer, and/or processing information sites such as ribosome binding sites, RNA binding sites, polyadenylation sites poly A addition of SV40 large T antigen), and transcription terminator sequences. See, for example, Ausubel et al., supra, Sambrook, et al., supra. proteins of the present invention are known and/or available, for example, from the American Type Culture Collection Catalog of Cell Lines and Hybridomas (www.atcc.org) or other known or commercial sources.

[00065] When eukaryotic host cells are employed, polyadenylation or transcriptional terminator sequences are typically incorporated into the vector. An example of a terminator sequence is the polyadenylation sequence from the bovine growth hormone gene. Sequences for proper transcriptional splicing may also be included. An example of a splicing sequence is a VP1 intron from SV40 (Sprague, et al., J. Virol. 45:773-781 (1983)). Additionally, gene sequences that control replication in the host cell can be incorporated into the vector, as is known in the art.

Purifying a Protein Framework

[00066] A protein scaffold can be recovered and purified from recombinant cell cultures by well-known methods including, but not limited to, protein A purification, ammonium sulfate or ethanol precipitation, acid extraction. , anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxy apatite chromatography and lectin chromatography. High performance liquid chromatography ("HPLC") can also be used for purification. See, for example, Colligan, Current Protocols in Immunology, or Current Protocols in Protein Science, John Wiley & Sons, NY, NY, USA, (1997-2001), for example, Chapters 1, 4, 6, 8, 9 and 10, each of which is incorporated herein by reference in its entirety.

[00067] Protein scaffolds of the present invention include naturally purified products, products of chemical synthesis procedures, and products produced by recombinant techniques from a prokaryotic or eukaryotic host including, for example, E. Coli, yeast, higher plants, insects and mammals. Depending on the host employed in a recombinant production procedure, the protein scaffold of the present invention may be glycosylated or non-glycosylated. These methods are described in many conventional laboratory manuals, such as Sambrook, supra, sections 17.37 to 17.42, Ausubel, supra, chapters 10, 12, 13, 16, 18 and 20, and Colligan, Protein Science, supra, chapters 12 to 14 , all of which are incorporated herein by reference in their entirety.

Amino Acid Codes

[00068] The amino acids that form the protein scaffolds of the present invention are often abbreviated. Amino acid designations may be indicated by designating the amino acid by its single-letter code, its three-letter code, its name, or one or more three-nucleotide codons as is well known in the art (see Alberts, B. et al. al., Molecular Biology of The Cell, Third Edition, Garland Publishing, Inc., New York, USA, 1994). A protein scaffold of the present invention may include one or more amino acid substitutions, deletions or additions, whether arising from natural mutations or human manipulation, as specified in the present invention. Amino acids in a protein scaffold of the present invention that are essential for its function can be identified using methods known in the art, such as site-directed mutagenesis or alanine scanning mutagenesis (e.g., Ausubel, supra, Chapters 8 and 15, Cunningham and Wells, Science 244:1081 to 1085 (1989)). The last cited procedure introduces unique alanine mutations at each of the residues in the molecule. The resulting mutant molecules are then tested for biological activity such as, but not limited to, at least one neutralizing activity. Sites that are critical for protein backbone binding can also be identified by structural analysis such as crystallization, nuclear magnetic resonance, or photoaffinity labeling (Smith, et al., J. Mol. Biol. 224:899 to 904 (1992) and de Vos, et al., Science 255:306 to 312 (1992)).

[00069] As will be understood by those skilled in the art, the present invention includes at least one biologically active protein scaffold of the present invention. Biologically active protein scaffolds have a specific activity of at least 20%, 30% or 40%, preferably at least 50%, 60% or 70%, and most preferably at least 80%, 90% or more. 95% to 1000% or more compared to native (non-synthetic), endogenous or related and known protein framework. Methods for testing and quantifying measurements of enzyme activity and substrate specificity are well known to those skilled in the art.

[00070] In another aspect, the invention relates to protein scaffolds and fragments, as described in the present invention, which are modified by covalently linking an organic moiety. This type of modification can produce a protein scaffold fragment with optimized pharmacokinetic properties (eg, increased in vivo serum half-life). The organic moiety can be a linear or branched hydrophilic polymeric group, a fatty acid group, or a fatty acid ester group. In particular embodiments, the hydrophilic polymeric group can have a molecular weight of from about 800 to about 120,000 Daltons and can be a polyalkane glycol (e.g., polyethylene glycol (PEG)), polypropylene glycol (PPG)), carbohydrate polymer, amino acid polymer or polyvinyl pyrrolidone, and the fatty acid or fatty acid ester group may comprise from about eight to about forty carbon atoms.

[00071] The modified protein scaffolds and fragments of the invention may comprise one or more organic moieties that are covalently linked, directly or indirectly, to the antibody. Each organic moiety which is linked to a scaffold or protein fragment of the invention may independently be a hydrophilic polymeric group, a fatty acid group or a fatty acid ester group. For use in the present invention, the term "fatty acid" encompasses monocarboxylic acids and dicarboxylic acids. For use in the present invention, the term "hydrophilic polymeric group" refers to an organic polymer that is more soluble in water than in octane. For example, polylysine is more soluble in water than in octane. Thus, a protein scaffold modified by the covalent linkage of polylysine is encompassed by the invention. Hydrophilic polymers suitable for modifying the protein scaffolds of the invention may be linear or branched and include, for example, polyalkane glycols (e.g., PEG, monomethoxy-polyethylene glycol (mPEG), PPG, and the like), carbohydrates (e.g., dextran, cellulose, oligosaccharides, polysaccharides and the like), hydrophilic amino acid polymers (for example, polylysine, polyarginine, polyaspartate and the like), polyalkane oxide (for example, polyethylene oxide, polypropylene oxide and the like) and polyvinyl pyrrolidone. Preferably, the hydrophilic protein scaffold modifying polymer of the invention has a molecular weight of from about 800 to about 150,000 Daltons, as a separate molecular entity. For example PEG5000 and PEG20000 can be used, where the subscript is the average molecular weight of the polymer in Daltons. The hydrophilic polymeric group may be substituted with one to about six alkyl, fatty acid, or fatty acid ester groups. Hydrophilic polymers that are substituted by a fatty acid or a fatty acid ester group can be prepared using suitable methods. For example, a polymer comprising an amine group can be coupled to a fatty acid carboxylate or fatty acid ester, and an activated carboxylate (e.g. activated with N,N-carbonyl diimidazole) to a fatty acid or fatty acid ester can be coupled to a hydroxyl group in a polymer.

[00072] Fatty acids and fatty acid esters suitable for modifying the protein scaffolds of the invention may be saturated or may contain one or more units of unsaturation. Fatty acids which are suitable for modifying protein scaffolds of the invention include, for example, n-dodecanoate (C12, laurate), n-tetradecanoate (C14, myristate), n-octadecanoate (C18, stearate), n-eicosanoate ( C20, arachidate), n-docosanoate (C22, behenate), n-triacontanoate (C30), n-tetracontanoate (C40), cis-Δ9-octadecanoate (C18, oleate), all cis-Δ5,8,11,14 -eicosatetraenoate (C20, arachidonate), octanedioic acid, tetradecanedioic acid, octadecanedioic acid, docosanedioic acid, and the like. Suitable fatty acid esters include monoesters of dicarboxylic acids which comprise a straight or branched lower alkyl group. The lower alkyl group may comprise from one to about twelve, preferably from one to about six, carbon atoms.

[00073] Modified protein scaffolds and fragments may be prepared using suitable methods, such as by reaction with one or more modifying agents. A "modifying agent", as the term is used in the present invention, refers to a suitable organic group (e.g., a hydrophilic polymer, a fatty acid, a fatty acid ester) that comprises an activating group. An "activating group" is a chemical moiety or functional group that can, under appropriate conditions, react with a second chemical group thereby forming a covalent bond between the modifying agent and the second chemical group. For example, amine-reactive activating groups include electrophilic groups such as tosylate, mesylate, halo (chloro, bromo, fluoro, iodo), N-hydroxysuccinimidyl (NHS) esters, and the like. Activating groups that can react with thiols include, for example, maleimide, iodo-acetyl, acryloyl, pyridyl disulfides, 5-thiol-2-nitrobenzoic acid thiol (TNB-thiol), and the like. An aldehyde functional group can be coupled to amine- or hydrazide-containing molecules, and an azide group can react with a trivalent phosphorous group to form phosphoramidate or phosphoramide bonds. Suitable methods for introducing activating groups into molecules are known in the art (see for example, Hermanson, G.T., Bioconjugate Techniques, Academic Press: San Diego, CA (1996)). An activating group may be attached directly to the organic group (e.g. hydrophilic polymer, fatty acid, fatty acid ester), or via a linker moiety, e.g. a divalent C1-C12 group in which one or more carbon atoms carbon can be replaced by a heteroatom, such as oxygen, nitrogen or sulfur. Suitable linking moieties include, for example, tetraethylene glycol, -(CH2)3-, -NH-(CH2)6-NH-, -(CH2)2-NH- and -CH2-O-CH2-CH2-O- CH2-CH2-O-CH-NH-. Modifying agents comprising a linker moiety can be produced, for example, by reacting a mono-Boc-alkyldiamine (e.g. mono-Boc-ethylenediamine, mono-Boc-diaminohexane) with a fatty acid in the presence of 1- ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) to form an amide bond between the free amine and the fatty acid carboxylate. The Boc protecting group can be removed from the product by treatment with trifluoroacetic acid (TFA) to expose a primary amine which can be coupled to another carboxylate as described, or it can be reacted with maleic anhydride and the resulting product is cyclized to produce a activated maleimido derivative of fatty acid. (See, for example, Thompson, et al., WO 92/16221, the teachings of which are incorporated herein by reference in their entirety.)

[00074] The modified protein scaffolds of the invention can be produced by reacting the scaffold or protein fragment with a modifying agent. For example, the organic moieties can be linked to a protein scaffold in a non-site-specific manner using an amine-reactive modifying agent, for example an NHS ester of PEG. Modified protein scaffolds and fragments that comprise an organic portion that is linked to specific sites of a protein scaffold of the present invention can be prepared using suitable methods such as reverse proteolysis ( Fisch et al., Bioconjugate Chem., 3: 147 to 153 (1992); Werlen et al., Bioconjugate Chem., 5:411 to 417 (1994); Kumaran et al., Protein Sci. 6(10):2233-2241 (1997); Itoh et al., Bioorg.Chem., 24(1): 59 to 68 (1996); Capellas et al., Biotechnol. Bioeng., 56(4):456 to 463 (1997 )), and the methods described in Hermanson, GT, Bioconjugate Techniques, Academic Press: San Diego, CA (1996).

Protein Framework Compositions Comprising Additional Therapeutically Active Ingredients

[00075] The protein scaffold compositions of the invention may optionally further comprise an effective amount of at least one compound or protein (small or large molecule) selected from at least one of an anti-infective drug, a drug for the cardiovascular (CV), a drug for the central nervous system (CNS), a drug for the autonomic nervous system (ANS), a drug for the respiratory tract, a drug for the gastrointestinal (GI) tract, a hormonal drug, a drug for fluid or electrolyte balance, a hematological drug, an antineoplastic, a drug for immunomodulation, a drug for ophthalmic, optical or nasal use, a drug for topical use, a nutritional drug or the like. Such drugs are well known in the art, including formulations, indications, dosage and administration for each of those disclosed in the present invention (see, for example, Nursing 2001 Handbook of Drugs, 21st Edition, Springhouse Corp., Springhouse, PA, USA, 2001, Health Professional's Drug Guide 2001, Editors, Shannon, Wilson, Stang, Prentice-Hall, Inc, Upper Saddle River, NJ, USA, Pharmacotherapy Handbook, Wells et al., Editors, Appleton & Lange, Stamford, CT, USA, each of which is incorporated herein by reference in their entirety).

[00076] The anti-infective drug may be at least one selected from amebicides, or at least one from antiprotozoa, anthelmintics, antifungals, antimalarials, antituberculin drugs or at least one from antileprotics, aminoglycosides, penicillins, cephalosporins, tetracyclines, sulfonamides, fluoroquinolones, antivirals, macrolide-based anti-infectives and assorted anti-infectives. The CV drug can be at least one selected from inotropics, antiarrhythmics, antianginals, antihypertensives, antilipemics and assorted cardiovascular drugs. The CNS drug can be at least one selected from non-narcotic analgesics, or at least one selected from antipyretics, non-steroidal anti-inflammatory drugs, narcotic analgesics or at least one opioid analgesic, sedative hypnotics, anticonvulsants, antidepressants, anti-anxiety drugs, antipsychotics, central nervous system stimulants, antiparkinsonians and assorted central nervous system drugs. The drug for ANS can be at least one selected from cholinergics (parasympathomimetics), anticholinergics, adrenergics (sympathomimetics), adrenergic blockers (sympatholytics), skeletal muscle relaxants, and neuromuscular blockers. The respiratory tract drug can be at least one selected from antihistamines, bronchodilators, expectorants or at least one antitussive, and assorted respiratory tract drugs. The drug for the GI tract can be at least one selected from antacids, or at least one adsorbent, or at least one antiflatulent, a digestive enzyme, or at least one gallstone solubilizer, antidiarrheals, laxatives, antiemetics, and antiulcer drugs. . The hormonal drug may be at least one selected from corticosteroids, androgens or at least one anabolic steroid, estrogen or at least one progestin, a gonadotropin, an antidiabetic drug or at least one glucagon, thyroid hormone, thyroid hormone antagonist, hormone of the pituitary and parathyroid-like drug. The fluid and electrolyte balance drug can be at least one selected from diuretics, electrolytes or at least one replacement solution, an acidifier or at least an alkalizer. The hematologic drug can be at least one selected from hematinics, anticoagulants, blood derivatives and thrombolytic enzymes. Antineoplastics can be at least one selected from alkylating drugs, antimetabolites, antibiotic antineoplastics, antineoplastics that alter the hormonal balance and various antineoplastics. The immunomodulatory drug can be at least one selected from immunosuppressants, vaccines, or at least one toxoid, an antitoxin, or at least one antivenom, an immune serum, and a biological response modifier. The ophthalmic, optic and nasal drugs can be at least one selected from ophthalmic anti-infectives, ophthalmic anti-inflammatory drugs, miotics, mydriatics, ophthalmic vasoconstrictors, and miscellaneous ophthalmic, optic and nasal drugs. The topical drug can be at least one selected from local anti-infectives, scabicides or at least one pediculicide or topical corticosteroid. The nutritional drug can be at least one selected from vitamins, minerals, or calories. See, for example, the contents of the Nursing 2001 Drug Handbook, above.

[00077] The at least one amebicide or antiprotozoan may be at least one selected from atovaquone, chloroquine hydrochloride, chloroquine phosphate, metronidazole, metronidazole hydrochloride and pentamidine isethionate. The at least one anthelmintic may be at least one selected from mebendazole, pyrantel pamoate and thiabendazole. The at least one antifungal may be at least one selected from amphotericin B, amphotericin B complex and cholesteryl sulfate, amphotericin B lipid complex, liposomal amphotericin B, fluconazole, flucytosine, micronized griseofulvin, ultramicronized griseofulvin, itraconazole, ketoconazole, nystatin and terbinafine hydrochloride. The at least one antimalarial may be at least one selected from chloroquine hydrochloride, chloroquine phosphate, doxycycline, chloroquine hydroxy sulfate, mefloquine hydrochloride, primaquine phosphate, pyrimethamine and pyrimethamine with sulfadoxine. The at least one antituberculin or antileprotic may be at least one selected from clofazimine, cycloserine, dapsone, ethambutol hydrochloride, isoniazid, pyrazinamide, rifabutin, rifampin, rifapentine and streptomycin sulfate. The at least one aminoglycoside may be at least one selected from amikacin sulfate, gentamicin sulfate, neomycin sulfate, streptomycin sulfate and tobramycin sulfate. The at least one penicillin can be at least one selected from amoxicillin/potassium clavulanate, amoxicillin trihydrate, ampicillin, ampicillin sodium, ampicillin trihydrate, ampicillin sodium/sulbactam sodium, cloxacillin sodium, dicloxacillin sodium, mezlocillin sodium, sodium nafcillin, sodium oxacillin, penicillin G benzathine, penicillin G potassium, penicillin G procaine, penicillin G sodium, penicillin V potassium, piperacillin sodium, piperacillin sodium/tazobactam sodium, ticarcillin disodium and ticarcillin disodium/clavulanate potassium. The at least one cephalosporin may be at least one selected from cefaclor, cefadroxil, cefazolin sodium, cefdinir, cefepime hydrochloride, cefixime, cefmetazol sodium, cefonicide sodium, cefoperazone sodium, cefotaxime sodium, cefotetam disodium, cefoxitin sodium, cefpodoxime proxetil, cefprozil, cefprozil ceftazidime, ceftibutene, ceftizoxime sodium, ceftriaxone sodium, cefuroxime axetil, cefuroxime sodium, cephalexin hydrochloride, cephalexin monohydrate, cephradine and loracarbefe. The at least one tetracycline can be at least one selected from demeclocycline hydrochloride, calcium doxycycline, doxycycline hyclate, doxycycline hydrochloride, doxycycline monohydrate, minocycline hydrochloride and tetracycline hydrochloride. The at least one sulfonamide may be at least one selected from co-trimoxazole, sulfadiazine, sulfamethoxazole, sulfisoxazole and acetyl sulfisoxazole. The at least one fluoroquinolone may be at least one selected from alatrofloxacin mesylate, ciprofloxacin, enoxacin, levofloxacin, lomefloxacin hydrochloride, nalidixic acid, norfloxacin, ofloxacin, sparfloxacin and trovafloxacin mesylate. The at least one fluoroquinolone may be at least one selected from alatrofloxacin mesylate, ciprofloxacin, enoxacin, levofloxacin, lomefloxacin hydrochloride, nalidixic acid, norfloxacin, ofloxacin, sparfloxacin and trovafloxacin mesylate. The at least one antiviral may be at least one selected from abacavir sulfate, acyclovir sodium, amantadine hydrochloride, amprenavir, cidofovir, delavirdine mesylate, didanosine, efavirenz, famciclovir, fomivirsen sodium, foscarnet sodium, ganciclovir, indinavir sulfate, lamivudine , lamivudine/zidovudine, nelfinavir mesylate, nevirapine, oseltamivir phosphate, ribavirin, rimantadine hydrochloride, ritonavir, saquinavir, saquinavir mesylate, stavudine, valaciclovir hydrochloride, zalcitabine, zanamivir and zidovudine. The at least one anti-infective macrolide may be at least one selected from azithromycin, clarithromycin, dirithromycin, erythromycin base, erythromycin estolate, erythromycin ethyl succinate, erythromycin lactobionate and erythromycin stearate. The at least one assorted anti-infective may be at least one selected from aztreonam, bacitracin, chloramphenicol sodium succinate, clindamycin hydrochloride, clindamycin palmitate hydrochloride, clindamycin phosphate, imipenem and cilastatin sodium, meropenem, nitrofurantoin macrocrystals, nitrofurantoin, quinupristine/dalfopristin, spectinomycin hydrochloride, trimethoprim and vancomycin hydrochloride (see, for example, pages 24 to 214 of the Nursing 2001 Drug Handbook.)

[00078] The at least one inotrope may be at least one selected from amrinone lactate, digoxin and milrinone lactate. The at least one antiarrhythmic may be at least one selected from adenosine, amiodarone hydrochloride, atropine sulfate, bretylium tosylate, diltiazem hydrochloride, disopyramide, disopyramide phosphate, esmolol hydrochloride, flecainide acetate, ibutilide fumarate, Lidocaine, Mexiletine Hydrochloride, Moricizine Hydrochloride, Phenytoin, Phenytoin Sodium, Procainamide Hydrochloride, Propafenone Hydrochloride, Propranolol Hydrochloride, Quinidine Bisulfate, Quinidine Gluconate, Quinidine Polygalacturonate, Quinidine Sulfate, Sotalol, Tocainide Hydrochloride and Hydrochloride of verapamil. The at least one antianginal may be at least one selected from amlodipidine besylate, amyl nitrite, bepridil hydrochloride, diltiazem hydrochloride, isosorbide dinitrate, isosorbide mononitrate, nadolol, nicardipine hydrochloride, nifedipine, nitroglycerin, propranolol hydrochloride, verapamil and verapamil hydrochloride. The at least one antihypertensive may be at least one selected from acebutolol hydrochloride, amlodipine besylate, atenolol, benazepril hydrochloride, betaxolol hydrochloride, bisoprolol fumarate, cylhexethyl candesartan, captopril, carteolol hydrochloride, carvedilol, clonidine , clonidine hydrochloride, diazoxide, diltiazem hydrochloride, doxazosin mesylate, enalaprilate, enalapril maleate, eprosartan mesylate, felodipine, fenoldopam mesylate, sodium fosinopril, guanabenz acetate, guanadrel sulfate, guanfacine hydrochloride, hydralazine hydrochloride, irbesartan, isradipine, labetalol hydrochloride, lisinopril, losartan potassium, methyldopa, methyldopate hydrochloride, metoprolol succinate, metoprolol tartrate, minoxidil, moexipril hydrochloride, nadolol, nicardipine hydrochloride, nifedipine, nisoldipine, sodium nitroprusside, penbutolol sulfate, perindopril erbumine, phentolamine mesylate, pindolol, prazosin hydrochloride, propranolol hydrochloride, quinapril hydrochloride, ramipril, telmisartan, terazosin hydrochloride, timolol maleate, trandolapril, valsartan and verapamil hydrochloride. The at least one antilipemic may be at least one selected from atorvastatin calcium, cerivastatin sodium, cholestyramine, colestipol hydrochloride, fenofibrate (micronised), fluvastatin sodium, gemfibrozil, lovastatin, niacin, pravastatin sodium and simvastatin. The at least one CV miscellaneous drug can be at least one selected from abciximab, alprostadil, arbutamine hydrochloride, cilostazol, clopidogrel bisulfate, dipyridamole, eptifibatide, midodrine hydrochloride, pentoxifylline, ticlopidine hydrochloride, Tirofiban hydrochloride. (See, for example, pages 215 to 336 of the Nursing 2001 Drug Handbook.)

[00079] The at least one non-narcotic analgesic or antipyretic may be at least one selected from acetaminophen, aspirin, magnesium choline trisalicylate, diflunisal and magnesium salicylate. The at least one non-steroidal anti-inflammatory drug may be at least one selected from celecoxib, diclofenac potassium, diclofenac sodium, etodolac, fenoprofen calcium, flurbiprofen, ibuprofen, indomethacin, indomethacin sodium trihydrate, ketoprofen, ketorolac tromethamine, nabumetone, naproxen, naproxen sodium, oxaprozin, piroxicam, rofecoxib and sulindac. The at least one narcotic or opioid analgesic may be at least one selected from alfentanil hydrochloride, buprenorphine hydrochloride, butophanol tartrate, codeine phosphate, codeine sulfate, fentanyl citrate, fentanyl transdermal patch, fentanyl transmucosal patch, hydrochloride hydromorphone, meperidine hydrochloride, methadone hydrochloride, morphine hydrochloride, morphine sulfate, morphine tartrate, nalbuphine hydrochloride, oxycodone hydrochloride, oxycodone pectinate, deoxymorphone hydrochloride, pentazocine hydrochloride, pentazocine hydrochloride and naloxone hydrochloride, pentazocine lactate, depropoxyphene hydrochloride, propoxyphene napsilate, remifentanil hydrochloride, sufentanil citrate and tramadol hydrochloride. The at least one sedative-hypnotic may be at least one selected from chloral hydrate, estazolam, flurazepam hydrochloride, pentobarbital, sodium pentobarbital, sodium phenobarbital, sodium secobarbital, temazepam, triazolam, zaleplom and zolpidem tartrate. The at least one anticonvulsant may be at least one selected from acetazolamide sodium, carbamazepine, clonazepam, chlorazepate dipotassium, diazepam, divalproex sodium, ethosuximide, fosphenytoin sodium, gabapentin, lamotrigine, magnesium sulfate, phenobarbital, phenobarbital sodium, phenytoin, phenytoin sodium, sodium phenytoin (extended), primidone, tiagabine hydrochloride, topiramate, sodium valproate and valproic acid. The at least one antidepressant may be at least one selected from amitriptyline hydrochloride, amitriptyline pamoate, amoxapine, bupropion hydrochloride, citalopram hydrobromide, clomipramine hydrochloride, desipramine hydrochloride, doxepin hydrochloride, fluoxetine hydrochloride, imipramine hydrochloride, pamoate of imipramine, mirtazapine, nefazodone hydrochloride, nortriptyline hydrochloride, paroxetine hydrochloride, phenelzine sulfate, sertraline hydrochloride, tranylcypromine sulfate, trimipramine maleate and venlafaxine hydrochloride. The at least one anti-anxiety drug may be at least one selected from alprazolam, buspirone hydrochloride, chlordiazepoxide, chlordiazepoxide hydrochloride, dipotassium chlorazepate, diazepam, doxepin hydrochloride, hydroxyzine embonate, hydroxyzine hydrochloride, hydroxyzine pamoate, lorazepam, meprobamate, midazolam hydrochloride and oxazepam. The at least one antipsychotic drug may be at least one selected from chlorpromazine hydrochloride, clozapine, fluphenazine decanoate, fluphenazine enanthate, fluphenazine hydrochloride, haloperidol, haloperidol decanoate, haloperidol lactate, loxapine hydrochloride, loxapine succinate , mesoridazine besylate, molindone hydrochloride, olanzapine, perphenazine, pimozide, prochlorperazine, quetiapine fumarate, risperidone, thioridazine hydrochloride, thiothixene, thiothixene hydrochloride and trifluoroperazine hydrochloride. The at least one central nervous system stimulant may be at least one selected from amphetamine sulfate, caffeine, dextroamphetamine sulfate, doxapram hydrochloride, methamphetamine hydrochloride, methylphenidate hydrochloride, modafinil, pemoline and phentermine hydrochloride. The at least one antiparkinsonian may be at least one selected from amantadine hydrochloride, benztropine mesylate, biperiden hydrochloride, biperiden lactate, bromocriptine mesylate, carbidopa-levodopa, entacapone, levodopa, pergolide mesylate, pramipexole dihydrochloride, ropinirole, selegiline hydrochloride, tolcapone and trihexylphenidyl hydrochloride. The at least one central nervous system miscellaneous drug may be at least one selected from bupropion hydrochloride, donepezil hydrochloride, droperidol, fluvoxamine maleate, lithium carbonate, lithium citrate, naratriptan hydrochloride, nicotine polacrylex, transdermal patch of nicotine, propofol, rizatriptan benzoate, sibutramine hydrochloride monohydrate, sumatriptan succinate, tacrine hydrochloride and zolmitriptan. (See, for example, pages 337 to 530 of the Nursing 2001 Drug Handbook.)

[00080] The at least one cholinergic (eg, parasympathomimetic) may be at least one selected from bethanechol chloride, edrophonium chloride, neostigmine bromide, neostigmine methyl sulfate, physostigmine salicylate and pyridostigmine bromide. The at least one anticholinergic may be at least one selected from atropine sulfate, dicyclomine hydrochloride, glycopyrrolate, hyoscyamine, hyoscyamine sulfate, propantheline bromide, scopolamine, butyl scopolamine bromide and scopolamine hydrobromide. The at least one adrenergic (sympathomimetic) may be at least one selected from dobutamine hydrochloride, dopamine hydrochloride, metaraminol bitartrate, norepinephrine bitartrate, phenylephrine hydrochloride, pseudoephedrine hydrochloride and pseudoephedrine sulfate. The at least one adrenergic (sympatholytic) blocker may be at least one selected from dihydroergotamine mesylate, ergotamine tartrate, methysergide maleate and propranolol hydrochloride. The at least one skeletal muscle relaxant can be at least one selected from baclofen, carisoprodol, chlorzoxazone, cyclobenzaprine hydrochloride, dantrolene sodium, methocarbamol and tizanidine hydrochloride. The at least one neuromuscular blocker may be at least one selected from atracurium besylate, cisatracurium besylate, doxacurium chloride, mivacurium chloride, pancuronium bromide, pipecuronium bromide, rapacuronium bromide, rocuronium bromide, succinylcholine chloride, tubocurarine chloride and vecuronium bromide. (See, for example, pages 531 to 84 of the Nursing 2001 Drug Handbook.)

[00081] The at least one antihistamine may be at least one selected from brompheniramine maleate, cetirizine hydrochloride, chlorpheniramine maleate, clemastine fumarate, cyproheptadine hydrochloride, diphenhydramine hydrochloride, fexofenadine hydrochloride, loratadine, hydrochloride of promethazine, promethazine theoclate, triprolidine hydrochloride. The at least one bronchodilator may be at least one selected from albuterol, albuterol sulfate, aminophylline, atropine sulfate, ephedrine sulfate, epinephrine, epinephrine bitartrate, epinephrine hydrochloride, ipratropium bromide, isoproterenol, isoproterenol hydrochloride, isoproterenol, levalbuterol hydrochloride, metaproterenol sulfate, oxtriphylline, pirbuterol acetate, salmeterol xinafoate, terbutaline sulfate and theophylline. The at least one expectorant or antitussive may be at least one selected from benzonatate, codeine phosphate, codeine sulfate, dextramethorphan hydrobromide, diphenhydramine hydrochloride, guaifenesin and hydromorphone hydrochloride. The at least one miscellaneous respiratory drug may be at least one selected from acetylcysteine, beclomethazone dipropionate, beractant, budesonide, calfactant, cromolyn sodium, dornase alfa, epoprostenol sodium, flunisolide, fluticasone propionate, montelukast sodium, nedocromyl sodium, palivizumab, triamcinolone acetonide, zafirlukast and zileutone. (See, for example, pages 585 to 642 of the Nursing 2001 Drug Handbook.)

[00082] The at least one antacid, adsorbent or antiflatulent may be at least one selected from aluminum carbonate, aluminum hydroxide, calcium carbonate, magaldrate, magnesium hydroxide, magnesium oxide, simethicone and sodium bicarbonate. The at least one digestive or gallstone solubilizing enzyme can be at least one selected from pancreatin, pancrelipase and ursodiol. The at least one antidiarrheal may be at least one selected from attapulgite, bismuth subsalicylate, calciumpolycarbophil, diphenoxylate hydrochloride and atropine sulfate, loperamide, octreotide acetate, tincture of opium and tincture of opium (camphor). The at least one laxative may be at least one selected from bisocodyl, polycarbophilic calcium, cascara sagrada, cascara sagrada fluid extract, cascara sagrada fluid extract, castor oil, calcium docusate, sodium docusate, glycerin, lactulose, magnesium citrate, magnesium hydroxide, magnesium sulfate, methyl cellulose, mineral oil, polyethylene glycol or electrolyte solution, plantago, senna and sodium phosphates. The at least one antiemetic may be at least one selected from chlorpromazine hydrochloride, dimenhydrinate, dolasetron mesylate, dronabinol, granisetron hydrochloride, meclizine hydrochloride, metocloproamide hydrochloride, ondansetron hydrochloride, perphenazine, prochlorperazine, prochlorperazine edisylate, prochlorperazine maleate, promethazine hydrochloride, scopolamine, thiethylperazine maleate and trimethobenzamide hydrochloride. The at least one anti-ulcer drug may be at least one selected from cimetidine, cimetidine hydrochloride, famotidine, lansoprazole, misoprostol, nizatidine, omeprazole, rabeprazole sodium, ranitidine bismuth citrate, ranitidine hydrochloride and sucralfate (see, for example, pages 643). to 95 of the Nursing 2001 Drug Handbook.)

[00083] The at least one corticosteroid may be at least one selected from betamethasone, betamethasone acetate or betamethasone sodium phosphate, cortisone acetate, dexamethasone, dexamethasone acetate, dexamethasone sodium phosphate, fludrocortisone acetate, hydrocortisone, hydrocortisone acetate , hydrocortisone cypionate, hydrocortisone sodium phosphate, hydrocortisone sodium succinate, methyl prednisolone, methyl prednisolone acetate, methyl prednisolone sodium succinate, prednisolone, prednisolone acetate, prednisolone sodium phosphate, prednisolone tebutate, prednisone, triamcinolone, acetonide triamcinolone and triamcinolone diacetate. The at least one androgen or anabolic steroid can be at least one selected from danazol, fluoxymesterone, methyltestosterone, nandrolone decanoate, nandrolone phenpropionate, testosterone, testosterone cypionate, testosterone enanthate, testosterone propionate and testosterone transdermal patch. The at least one estrogen or progestin may be at least one selected from esterified estrogens, estradiol, estradiol cypionate, estradiol/norethindrone acetate transdermal patch, estradiol valerate, estrogens (conjugates), estropipate, ethinyl estradiol, ethinyl estradiol, and desogestrel, ethinyl estradiol and ethynodiol diacetate, ethinyl estradiol and desogestrel, ethinyl estradiol and ethynodiol diacetate, ethinyl estradiol and levonorgestrel, ethinyl estradiol and norethindrone, ethinyl estradiol and norethindrone acetate, ethinyl estradiol and norgestimate, ethinyl estradiol and norgestrel, ethinyl estradiol and norethindrone and ferrous acetate and fumarate, levonorgestrel, medroxy progesterone acetate, mestranol and norethindrone, norethindrone, norethindrone acetate, norgestrel and progesterone. The at least one gonadrotropin can be at least one selected from ganirelix acetate, gonadorelin acetate, histrelin acetate and menotropins. The at least one antidiabetic or glucagon may be at least one selected from acarbose, chlorpropamide, glimepiride, glipizide, glucagon, glyburide, insulins, metformin hydrochloride, miglitol, pioglitazone hydrochloride, repaglinide, rosiglitazone maleate and troglitazone. The at least one thyroid hormone may be at least one selected from levothyroxine sodium, liothyronine sodium, liothrix and thyroid. The at least one thyroid hormone antagonist may be at least one selected from methimazole, potassium iodide, potassium iodide (saturated solution), propylthiouracil, radioactive iodine (131I sodium iodide) and strong iodine solution. The at least one pituitary hormone may be at least one selected from corticotropin, cosyntropin, desmopressin acetate, leuprolide acetate, repository corticotropin, somatrem, somatropin and vasopressin. The at least one parathyroid-like drug can be at least one selected from calcifediol, calcitonin (human), calcitonin (from salmon), calcitriol, dihydrotachysterol and disodium etidronate. (See, for example, pages 696 to 796 of the Nursing 2001 Drug Handbook.)

[00084] The at least one diuretic may be at least one selected from acetazolamide, sodium acetazolamide, amiloride hydrochloride, bumetanide, chlorthalidone, sodium ethacrynate, ethacrynic acid, furosemide, hydrochlorothiazide, indapamide, mannitol, metolazone, spirono lactone, torsemide, triamterene and urea. The at least one electrolyte or replacement solution may be at least one selected from calcium acetate, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, calcium lactate, calcium phosphate. calcium (dibasic), calcium phosphate (tribasic), dextran (high molecular weight), dextran (low molecular weight), hetamide, magnesium chloride, magnesium sulfate, potassium acetate, potassium bicarbonate, potassium chloride, potassium gluconate potassium, Ringer's injection, Ringer's injection (lactate) and sodium chloride. The at least one acidifier or alkalizer may be at least one selected from sodium bicarbonate, sodium lactate and tromethamine. (See, for example, pages 797 to 833 of the Nursing 2001 Drug Handbook.)

[00085] The at least one hematin may be at least one selected from ferrous fumarate, ferrous gluconate, ferrous sulfate, ferrous sulfate (dry), iron dextran, iron sorbitol, polysaccharide-iron complex, and sodium ferric gluconate complex. The at least one anticoagulant may be at least one selected from ardeparin sodium, dalteparin sodium, danaparoid sodium, enoxaparin sodium, heparin calcium, heparin sodium and warfarin sodium. The at least one blood derivative may be at least one selected from 5% albumin, 25% albumin, anti-hemophilic factor, anti-inhibitor clotting complex, antithrombin III (human), factor IX (human), factor complex IX, and plasma protein fractions. The at least one thrombolytic enzyme can be at least one selected from alteplase, anistreplase, reteplase (recombinant), streptokinase and urokinase. (See, for example, pages 834 to 66 of the Nursing 2001 Drug Handbook.)

[00086] The at least one alkylating drug may be at least one selected from busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cyclophosphamide, ifosfamide, lomustine, mechlorethamine hydrochloride, melphalan, melphalan hydrochloride, streptozocin, temozolomide and thiotepa. The at least one antimetabolite may be at least one selected from capecitabine, cladribine, cytarabine, floxuridine, fludarabine phosphate, fluorouracil, hydroxyurea, mercaptopurine, methotrexate, sodium methotrexate and thioguanine. The at least one antineoplastic antibiotic may be at least one selected from bleomycin sulfate, dactinomycin, liposomal daunorubicin citrate, daunorubicin hydrochloride, doxorubicin hydrochloride, liposomal doxorubicin hydrochloride, epirubicin hydrochloride, idarubicin hydrochloride, mitomycin, pentostatin, plicamycin and valrubicin. The at least one hormone-altering antineoplastic may be at least one selected from anastrozole, bicalutamide, estramustine sodium phosphate, exemestane, flutamide, goserelin acetate, letrozole, leuprolide acetate, megestrol acetate, nilutamide, tamoxifen citrate, testosterone and toremifene citrate. The at least one assorted antineoplastic may be at least one selected from asparaginase, bacillus Calmette-Guerin (BCG) (live intravesical), dacarbazine, docetaxel, etoposide, etoposide phosphate, gemcitabine hydrochloride, irinotecan hydrochloride, mitotane, hydrochloride of mitoxantrone, paclitaxel, pegaspargas, porfimer sodium, procarbazine hydrochloride, rituximab, teniposide, topotecan hydrochloride, trastuzumab, tretinoin, vinblastine sulfate, vincristine sulfate, vinorelbine tartrate. (See, for example, pages 867 to 963 of the Nursing 2001 Drug Handbook.)

[00087] The at least one immunosuppressant may be at least one selected from azathioprine, basiliximab, cyclosporine, daclizumab, lymphocyte immunoglobulin, muromonab-CD3, mycophenolate mofetil, mycophenolate mofetil hydrochloride, sirolimus and tacrolimus. The at least one vaccine or toxoid may be at least one selected from BCG vaccine, cholera vaccine, diphtheria and tetanus toxoids (adsorbed), diphtheria and tetanus toxoids, and acellular adsorbed pertussis vaccine, diphtheria and tetanus toxoids, and vaccine with whole cell pertussis, conjugate vaccines for Haemophilus b, vaccine for hepatitis A (inactivated), vaccine for hepatitis B (recombinant), vaccine for influenza virus 1999 to 2000 trivalent types A & B (purified surface antigen), vaccine for influenza virus 1999 to 2000 trivalent types A & B (subvirion or purified subvirion), influenza virus vaccine 1999 to 2000 trivalent types A & B (whole virion), Japanese encephalitis virus vaccine (inactivated), Lyme (recombinant OspA), rubella, measles and mumps vaccine (live), rubella, measles and mumps vaccine (live attenuated), measles virus vaccine (live attenuated), meningococcal-based vaccine and polysaccharide, mumps virus vaccine (live), bubonic plague vaccine, pneumococcal vaccine (polyvalent), poliovirus vaccine (inactivated), poliovirus vaccine (live, oral, trivalent), rabies vaccine (adsorbed), vaccine for rabies (human diploid cell), mumps and rubella virus vaccine (live), rubella virus vaccine (live, attenuated), tetanus toxoid (adsorbed), tetanus toxoid (fluid), typhoid vaccine (oral) ), typhoid vaccine (parenteral), typhoid polysaccharide vaccine VI, varicella virus vaccine and yellow fever vaccine. The at least one antitoxin or antivenom can be at least one selected from black widow spider antivenom, Crotalidae antivenom (polyvalent), diphtheria antitoxin (equine) and Micrurus fulvius antivenom. The at least one immune serum may be at least one selected from cytomegalovirus immunoglobulin (intravenous), hepatitis B immunoglobulin (human), intramuscular immunoglobulin, intravenous immunoglobulin, rabies immunoglobulin (human), intravenous respiratory syncytial virus immunoglobulin (human) , Rh0(D) immunoglobulin (human), intravenous Rh0(D) immunoglobulin (human), tetanus immunoglobulin (human), and varicella-zoster immunoglobulin. The at least one biological response modifier may be at least one selected from aldesleukin, epoetin alfa, filgrastim, glatiramer acetate for injection, interferon alfacon-1, interferon alfa-2a (recombinant), interferon alfa-2b (recombinant), interferon beta-1a, interferon beta-1b (recombinant), interferon gamma-1b, levamisole hydrochloride, oprelvecin and sargramostim. (See, for example, pages 964 to 1040 of the Nursing 2001 Drug Handbook.)

[00088] The at least one anti-infective for ophthalmic use can be selected from bacitracin, chloramphenicol, ciprofloxacin hydrochloride, erythromycin, gentamicin sulfate, 0.3% ofloxacin, polymyxin B sulfate, 10% sodium sulfacetamide, sulfacetamide 15% sodium, 30% sodium sulfacetamide, tobramycin and vidarabine. The at least one anti-inflammatory for ophthalmic use may be at least one selected from dexamethasone, dexamethasone sodium phosphate, 0.1% sodium diclofenac, fluorometholone, flurbiprofen sodium, ketorolac tromethamine, prednisolone acetate (suspension) and phosphate prednisolone sodium (solution). The at least one miotic can be at least one selected from acetylcholine chloride, carbachol (intraocular), carbachol (topical), echothiophate iodide, pilocarpine, pilocarpine hydrochloride and pilocarpine nitrate. The at least one mydriatic may be at least one selected from atropine sulfate, cyclopentolate hydrochloride, epinephrine hydrochloride, epinephrine borate, homatropine hydrobromide, phenylephrine hydrochloride, scopolamine hydrobromide and tropicamide. The at least one ophthalmic vasoconstrictor may be at least one selected from naphazoline hydrochloride, oxymetazoline hydrochloride and tetrahydrozoline hydrochloride. The at least one ophthalmic miscellaneous may be at least one selected from apraclonidine hydrochloride, betaxolol hydrochloride, brimonidine tartrate, carteolol hydrochloride, dipivefrine hydrochloride, dorzolamide hydrochloride, emedastine difumarate, sodium fluorescein, ketotifen fumarate, latanoprost, levobunolol hydrochloride, metipranolol hydrochloride, sodium chloride (hypertonic) and timolol maleate. The at least one optic may be at least one selected from boric acid, chloramphenicol carbamide peroxide, polypeptide triethanolamine oleate condensate. The at least one nasal drug may be at least one selected from beclomethasone dipropionate, budesonide, ephedrine sulfate, epinephrine hydrochloride, flunisolide, fluticasone propionate, naphazoline hydrochloride, oxymetazoline hydrochloride, phenylephrine hydrochloride, tetrahydrozoline hydrochloride , triamcinolone acetonide, xylometazoline hydrochloride. (See, for example, pages 1041 to 97 of the Nursing 2001 Drug Handbook.)

[00089] The at least one local anti-infective may be at least one selected from acyclovir, amphotericin B, azelaic acid cream, bacitracin, butoconazole nitrate, clindamycin phosphate, clotrimazole, econazole nitrate, erythromycin, gentamicin sulfate, ketoconazole, mafenide acetate, metronidazole (topical), miconazole nitrate, mupirocin, naftifine hydrochloride, neomycin sulfate, nitrofurazone, nystatin, silver sulfadiazine, terbinafine hydrochloride, terconazole, tetracycline hydrochloride, thioconazole and tolnaftate. The at least one scabicide or pediculicide can be at least one selected from crotamitone, lindane, permethrin and pyrethrins. The at least one topical corticosteroid may be at least one selected from betamethasone dipropionate, betamethasone valerate, clobetasol propionate, desonide, desoxymethasone, dexamethasone, dexamethasone sodium phosphate, diflorasone diacetate, fluocinolone acetonide, fluocinonide, flurandrenolide, fluticasone propionate, halcionide, hydrocortisone, hydrocortisone acetate, hydrocortisone butyrate, hydrocortisone valerate, mometasone furoate and triamcinolone acetonide. (See, for example, pages 1098 to 1136 of the Nursing 2001 Drug Handbook.)

[00090] The at least one vitamin or one mineral may be at least one selected from vitamin A, vitamin B complex, cyanocobalamin, folic acid, hydroxycobalamin, calcium leucovorin, niacin, niacinamide, pyridoxine hydrochloride, riboflavin, thiamine hydrochloride, vitamin C, vitamin D, cholecalciferol, ergocalciferol, vitamin D analogue, doxercalciferol, paricalcitol, vitamin E, vitamin K analogue, phytonadione, sodium fluoride, sodium fluoride (topical), trace elements, chromium, copper, iodine, manganese, selenium and zinc. The at least one caloric can be at least one selected from amino acid infusions (crystalline), amino acid infusions in dextrose, amino acid infusions with electrolytes, amino acid infusions with electrolytes in dextrose, amino acid infusions for liver failure, amino acid infusions for high metabolic stress, amino acid infusions for kidney failure, dextrose, fat emulsions and medium chain triglycerides. (See, for example, pages 1137 to 63 of the Nursing 2001 Drug Handbook.)

[00091] The protein scaffold compositions of the present invention may further comprise at least one of any suitable and effective amount of a composition or pharmaceutical composition comprising a protein scaffold brought into contact with, or administered to, a cell, a tissue, a organ, an animal or a patient in need of such modulation, treatment or therapy, optionally further comprising at least one selected from at least one TNF antagonist (for example, but not limited to, a chemical or protein antagonist of TNF, a TNF monoclonal or polyclonal antibody or fragment thereof, a soluble TNF receptor (e.g. p55, p70 or p85) or fragment thereof, fusion polypeptides thereof, or a small molecule TNF antagonist, e.g. a TNF binding protein I or II (TBP-1 or TBP-II), nerelimomab, infliximab, etanercept, CDP-571, CDP-870, afelimomab, lenercept, and the like), an antirheumatic co (eg, methotrexate, auranofin, aurothioglucose, azathioprine, etanercept, gold sodium thiomalate, hydroxychloroquine sulfate, leflunomide, sulfasalazine), a muscle relaxant, a narcotic, a non-steroidal anti-inflammatory drug (NSAID), an analgesic, a anaesthetic, a sedative, a local anesthetic, a neuromuscular blocker, a microbicide (e.g., an aminoglycoside, a fungicide, an antiparasitic, an antiviral, a carbapenem, a cephalosporin, a fluoroquinolone, a macrolide, a penicillin, a sulfonamide, a tetracycline, another microbicide), an antipsoriasis, a corticosteroid, an anabolic steroid, a diabetes-related agent, a mineral, a nutritional agent, a thyroid agent, a vitamin, a calcium-related hormone, an antidiarrheal, an antitussive, an antiemetic, an antiulcer, a laxative, an anticoagulant, an erythropoietin (eg, epoetin alfa), a filgrastim (eg, G-CSF, Neupogen), a sargramosti m (GM-CSF, Leukine), an immunization, an immunoglobulin, an immunosuppressant (eg, basiliximab, cyclosporine, daclizumab), a growth hormone, a hormone replacement drug, an estrogen receptor modulator, a mydriatic , a cycloplegic, an alkylating agent, an antimetabolite, a mitotic inhibitor, a radiopharmaceutical, an antidepressant, an antimanic agent, an antipsychotic, an anxiolytic, a hypnotic, a sympathomimetic, a stimulant, donepezil, tacrine, an asthma drug, a beta agonist, an inhaled steroid, a leukotriene inhibitor, a methylxanthine, a cromolyn, an epinephrine or analogue thereof, dornase alfa (Pulmozyme), a cytokine or a cytokine antagonist. Some non-limiting examples of such cytokines include, but are not limited to, any of IL-1 to IL-32 (e.g., IL-1, IL-2, etc.). Suitable dosages are well known in the art. See, for example, Wells et al., editors, Pharmacotherapy Handbook, 2nd Edition, Appleton and Lange, Stamford, CT, USA (2000), PDR Pharmacopoeia, Tarascon Pocket Pharmacopoeia 2000, Deluxe Edition, Tarascon Publishing, Loma Linda, CA , USA (2000), each of which is incorporated herein by reference in their entirety.

[00092] Such anti-cancer or anti-infective substances may also include toxin molecules that are associated, linked, co-formulated or co-administered with at least one protein scaffold of the present invention. The toxin may optionally act to selectively kill pathological cells or tissues. The pathological cell can be a cancer cell or another cell. Such toxins may be, but are not limited to, a purified or recombinant toxin or toxin fragment that comprises at least one toxin functional cytotoxic domain, e.g. selected from at least one of ricin, diphtheria toxin, a poisonous toxin , or a bacterial toxin. The term toxin also includes both endotoxins and exotoxins produced by any naturally occurring, mutant or recombinant bacteria or virus that can cause any pathological condition in humans and other mammals, including toxin shock, which can result in death. Such toxins may include, but are not limited to, E. coli heat-labile enterotoxigenic enterotoxin (LT), heat-stable enterotoxin (ST), shiguela cytotoxin, Aeromonas enterotoxins, toxic shock syndrome toxin-1 (TSST-1). ), Staphylococcal enterotoxin A (SEA), B (SEB), or C (SEC), Streptococcal enterotoxin and the like. Such bacteria include, but are not limited to, strains of an E. coli enterotoxigenic (ETEC) species, E. coli enterohemorrhagic (e.g., strains of serotype 0157:H7), staphylococcal species (e.g., Staphylococcus aureus, Staphylococcus pyogenes), Shigella species (e.g. Shigella dysenteriae, Shigella flexneri, Shigella boydii, and Shigella sonnei), Salmonella species (e.g. Salmonella typhi, Salmonella cholera-suis, Salmonella enteritidis), Clostridium species (e.g. Clostridium perfringens, Clostridium difficile, Clostridium botulinum), Camphlobacter species (e.g. Camphlobacter jejuni, Camphlobacter fetus), Heliobacter species, (e.g. Heliobacter pylori), Aeromonas species (e.g. Aeromonas sobria, Aeromonas hydrophila, Aeromonas caviae), Pleisomonas shigelloides, Yersina enterocolitica, Vibrios species (eg Vibrios cholerae, Vibrios parahemolyticus), Klebsiella species, Pseudomonasaeruginosa and Streptococci. See, for example, Stein, ed., INTERNAL MEDICINE, 3rd ed, pages 1 to 13, Little, Brown and Co., Boston, (1990); Evans et al., eds., Bacterial Infections of Humans: Epidemiology and Control, 2nd Ed., pp 239-254, Plenum Medical Book Co., New York, USA (1991); Mandell et al, Principles and Practice of Infectious Diseases, 3rd Ed., Churchill Livingstone, New York, USA (1990); Berkow et al, eds., The Merck Manual, 16th edition, Merck and Co., Rahway, N.J., 1992; Wood et al, FEMS Microbiology Immunology, 76:121-134 (1991); Marrack et al, Science, 248:705-711 (1990), the contents of which are incorporated herein in their entirety by reference.

[00093] The compounds, compositions or protein scaffold combinations of the present invention may additionally comprise at least one of any suitable auxiliary, including, but not limited to, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like. Pharmaceutically acceptable auxiliaries are preferred. Some non-limiting examples of such sterile solutions, and methods for preparing the same, are well known in the art including, but not limited to, Gennaro, Editors, Remington's Pharmaceutical Sciences, 18th Edition, Mack Publishing Co. (Easton, PA, USA) 1990. Pharmaceutically acceptable carriers can be routinely selected that are suitable for the mode of administration, solubility and/or stability of the protein scaffold composition, fragment or variant thereof, as is well known in the art or as described in the present invention. .

[00094] Pharmaceutical excipients and additives useful in the present composition include, but are not limited to, proteins, peptides, amino acids, lipids and carbohydrates (for example, sugars, including monosaccharides, di-, tri-, tetra- and oligosaccharides, sugars derivatives such as alditols, aldonic acids, esterified sugars and the like, and sugar polysaccharides or polymers), which may be present alone or in combination, and which comprise, alone or in combination, from 1 to 99.99 %, by weight or volume. Examples of protein-based excipients include serum albumin such as human serum albumin (HSA), recombinant human albumin (rHA), gelatin, casein and the like. Representative amino acid/protein components, which may also function as a buffer, include alanine, glycine, arginine, betaine, histidine, glutamic acid, aspartic acid, cysteine, lysine, leucine, isoleucine, valine, methionine, phenylalanine, aspartame and the like. . A preferred amino acid is glycine.

[00095] Carbohydrate-based excipients suitable for use in the invention include, for example, monosaccharides such as fructose, maltose, galactose, glucose, D-mannose, sorbose and the like, disaccharides such as lactose, sucrose, trehalose, cellobiose and the like. , polysaccharides such as raffinose, melezitose, maltodextrins, dextrans, starches and the like, and alditols such as mannitol, xylitol, maltitol, lactitol, xylitol, sorbitol (glucitol), myoinositol and the like. Preferred carbohydrate excipients for use in the present invention are mannitol, trehalose, and raffinose.

[00096] Protein scaffold compositions may also include a buffer or a pH adjusting agent, typically the buffer being a salt prepared from an organic acid or base. Representative buffers include salts of organic acid, such as salts of citric acid, ascorbic acid, gluconic acid, carbonic acid, tartaric acid, succinic acid, acetic acid, or phthalic acid; Tris, tromethamine hydrochloride or phosphate buffers. Preferred buffers for use in the present compositions are organic acid salts such as citrate.

[00097] Additionally, protein scaffold compositions of the invention may include polymeric excipients/additives such as polyvinylpyrrolidones, Ficoll (a polymeric sugar), dextrates (e.g. cyclodextrins such as 2-hydroxypropyl-β-cyclodextrin), polyethylene glycols , flavoring agents, microbicidal agents, sweeteners, antioxidants, antistatic agents, surfactants (e.g. polysorbates such as "TWEEN 20" and "TWEEN 80"), lipids (e.g. phospholipids, fatty acids), steroids (e.g. cholesterol ) and chelating agents (eg EDTA).

[00098] These and other known pharmaceutical excipients and/or additives suitable for use in the protein scaffold compositions, portions or variants thereof, in accordance with the present invention are known in the art, for example as mentioned in "Remington: The Science & Practice of Pharmacy", 19th Edition, Williams & Williams, (1995), and in "Physician's Desk Reference", 52nd Edition, Medical Economics, Montvale, NJ, USA (1998), the disclosures of which are incorporated herein by reference, in its entirety. Preferred carrier or excipient materials are carbohydrates (e.g. saccharides and alditols) and buffers (e.g. citrate) or polymeric agents. An exemplary carrier molecule consists of a mucopolysaccharide, hyaluronic acid, which may be useful for intra-articular application.

Formulations

[00099] As noted above, the invention features stable formulations, which preferably comprise a phosphate buffer with saline or a chosen salt, as well as preserved solutions and formulations containing a preservative, as well as multipurpose preserved formulations suitable for use. pharmaceutical or veterinary, comprising at least one protein scaffold in a pharmaceutically acceptable formulation. Preserved formulations contain at least one known preservative or optionally selected from the group consisting of at least one phenol, m-cresol, p-cresol, o-cresol, chlorocresol, benzyl alcohol, phenylmercuric nitrite, phenoxyethanol, formaldehyde, chlorobutanol, chloride magnesium (e.g. hexahydrate), alkyl paraben (methyl, ethyl, propyl, butyl and the like), benzalkonium chloride, benzethonium chloride, sodium dehydroacetate and thimerosal, polymers, or mixtures thereof in an aqueous diluent. Any suitable concentration or mixture, as known in the art, such as about 0.0015%, or any range, value, or fraction thereof, may be used. Some non-limiting examples include, no preservative, about 0.1 to 2% m-cresol (e.g. 0.2, 0.3, 0.4, 0.5, 0.9, 1.0%) , about 0.1 to 3% benzyl alcohol (eg, 0.5, 0.9, 1.1, 1.5, 1.9, 2.0, 2.5%), about 0.001 0.5% thimerosal (eg, 0.005, 0.01), about 0.001 to 2.0% phenol (eg, 0.05, 0.25, 0.28, 0.5, 0.9 , 1.0%), 0.0005 to 1.0% alkylparaben(s) (e.g., 0.00075, 0.0009, 0.001, 0.002, 0.005, 0.0075, 0.009, 0.01, 0, 02, 0.05, 0.075, 0.09, 0.1, 0.2, 0.3, 0.5, 0.75, 0.9, 1.0%), and the like.

[000100] As noted above, the invention features an article of manufacture comprising packaging material and at least one vial comprising a solution of at least one protein scaffold with the prescribed buffers and/or preservatives, optionally in an aqueous diluent, wherein said packaging material comprises a label indicating that this solution can be maintained over a period of 1, 2, 3, 4, 5, 6, 9, 12, 18, 20, 24, 30, 36, 40, 48, 54, 60, 66 or 72 hours or more. The invention further comprises an article of manufacture comprising packaging material, a first vial comprising at least one lyophilized protein scaffold, and a second vial comprising an aqueous diluent with the prescribed buffer or preservative, said packaging material comprising a label that instructs a patient to reconstitute the at least one protein scaffold in the aqueous diluent to form a solution that can be maintained over a period of twenty-four hours or more.

[000101] The at least one protein scaffold used in accordance with the present invention may be produced by recombinant means, including from mammalian cells or transgenic preparations, or may be purified from other biological sources, as described in the present invention or as known in the art.

[000102] The range of contents of the at least one protein scaffold in the product of the present invention includes amounts which, after reconstitution in the case of a wet/dry system, result in concentrations from about 1.0 μg/ml to about 1,000 mg/ml, although lower or higher concentrations are functional and depend on the application vehicle for which the product is intended, for example solution formulations will be different from those for transdermal patches, or pulmonary, transmucosal, osmotic or by micropump.

[000103] Preferably, the aqueous diluent optionally further comprises a pharmaceutically acceptable preservative. Preferred preservatives include those selected from the group consisting of phenol, m-cresol, p-cresol, o-cresol, chlorocresol, benzyl alcohol, alkyl paraben (methyl, ethyl, propyl, butyl and the like), benzalkonium chloride, benzethonium chloride, sodium dehydroacetate and thimerosal, or mixtures thereof. The concentration of preservative used in the formulation is a concentration sufficient to result in a microbicidal effect. Such concentrations are dependent on the preservative selected and are readily determined by those skilled in the art.

[000104] Other excipients, for example isotonicity agents, buffers, antioxidants and enhancing preservatives, may optionally and preferably be added to the diluent. An isotonicity agent such as glycerin is commonly used in known concentrations. A physiologically tolerated buffer is preferably added to provide improved pH control. The formulations can cover a wide range of pHs, such as from about pH 4 to about pH 10, preferred ranges from about pH 5 to about pH 9, and a most preferred range from about 6.0 to about pH 9. 8.0. Preferably, the formulations of the present invention have a pH between about 6.8 and about 7.8. Preferred buffers include phosphate buffers and, most preferably, sodium phosphate, particularly phosphate buffered saline (PBS).

[000105] Other additives such as pharmaceutically acceptable solubilizers such as Tween 20 (polyoxyethylene (20) sorbitan monolaurate), Tween 40 (polyoxyethylene (20) sorbitan monopalmitate), Tween 80 (polyoxyethylene (20) sorbitan monooleate), Pluronic F68 (polyoxyethylene and polyoxypropylene block copolymers) and PEG (polyethylene glycol), or non-ionic surfactants such as polysorbate 20 or 80, or poloxamer 184 or 188, Pluronic® polyols, other block copolymers, and chelators such as EDTA and EGTA, may optionally be added to formulations or compositions to reduce aggregation. These additives are particularly useful if a pump or plastic container is used to deliver the formulation. The presence of a pharmaceutically acceptable surfactant attenuates the propensity of the protein to aggregate.

[000106] The formulations of the present invention may be prepared by a process comprising mixing at least one protein scaffold and a preservative selected from the group consisting of phenol, m-cresol, p-cresol, o-cresol, chlorocresol, alcohol benzyl, alkyl paraben, (methyl, ethyl, propyl, butyl and the like), benzalkonium chloride, benzethonium chloride, sodium dehydroacetate and thimerosal, or mixtures thereof, in an aqueous diluent. The mixing of the at least one protein scaffold and a preservative in an aqueous diluent is done using conventional dissolution and mixing procedures. To prepare a suitable formulation, for example, a measured amount of at least one scaffold of protein in buffered solution is combined with the desired preservative in buffered solution in amounts sufficient to provide the protein and preservative at the desired concentrations. Variations of this process will be recognized by one of skill in the art. For example, the order in which the components are added, the use of additional additives, and the temperature and pH at which the formulation is prepared are factors that can be optimized for the concentration and means of administration used.

[000107] The claimed formulations may be supplied to patients in the form of clear solutions or in the form of double vials comprising a vial containing at least one lyophilized protein scaffold, which is reconstituted with a second vial containing water, a preservative and/or or excipients, preferably a phosphate buffer and/or saline and a chosen salt, in an aqueous diluent. Either a single vial of solution, or a double vial that requires reconstitution, can be reused multiple times and may be sufficient for a single cycle or multiple cycles of patient care and thus may provide a more convenient treatment regimen than the currently available.

[000108] The present claimed articles of manufacture are useful for administering a period that is in the range from immediate to twenty-four hours or more. Accordingly, the presently claimed articles of manufacture offer significant advantages to the patient. Formulations of the invention may optionally be safely stored at temperatures from about 2°C to about 40°C, and retain the protein's biological activity for extended periods of time, thus allowing the use of a package label indicating that the solution can be held and/or used over a period of 6, 12, 18, 24, 36, 48, 72 or 96 hours, or longer. If a preservative diluent is used, this label may include use for 1 to 12 months, half a year, a year and a half and/or two years.

[000109] Solutions of at least one protein scaffold of the invention may be prepared by a process comprising mixing at least one protein scaffold in an aqueous diluent. Mixing is carried out using conventional dissolving and mixing procedures. To prepare a suitable diluent, for example, a measured amount of at least one scaffold of protein in water or buffer is combined in an amount sufficient to provide the protein and, optionally, a preservative or buffer, at the desired concentrations. Variations of this process will be recognized by one of skill in the art. For example, the order in which the components are added, the use of additional additives, and the temperature and pH at which the formulation is prepared are factors that can be optimized for the concentration and means of administration used.

[000110] The claimed products can be supplied to patients in the form of clear solutions or in the form of double vials comprising a vial containing at least one lyophilized protein scaffold which is reconstituted with a second vial containing the aqueous diluent. Either a single vial of solution, or a double vial that requires reconstitution, can be reused multiple times and may be sufficient for a single cycle or multiple cycles of the patient's treatment and thus provide a more convenient treatment regimen than the currently available.

[000111] The claimed products may be provided indirectly to patients by supplying pharmacies, clinics or other institutions and facilities with clear solutions or double vials comprising a vial of at least one lyophilized protein scaffold, which is reconstituted with a second vial containing the aqueous diluent. The clear solution, in this case, can be up to a liter or even a larger size, providing a large reservoir from which smaller portions of the solution of at least one protein scaffold can be withdrawn once or several times and transferred to smaller flasks at be provided by pharmacies or clinics to their customers and/or patients.

[000112] Recognized devices comprising single vial systems include pen-type injector devices for application of a solution, such as BD Pens, BD Autojector®, Humaject®, NovoPen®, BD®Pen, AutoPen®, and OptiPen®, GenotropinPen® , Genotronorm Pen®, Humatro Pen®, Reco-Pen®, Roferon Pen®, Biojector®, Iject®, J-tip Needle-Free Injector®, Intraject®, Medi-Ject®, for example, such as those developed by Becton Dickensen (Franklin Lakes, NJ, USA, www.bectondickenson.com), Disetronic (Burgdorf, Switzerland, www.disetronic.com; Bioject, Portland, Oregon, USA (www.bioject.com); National Medical Products, Weston Medical (Peterborough , UK, www.weston-medical.com), Medi-Ject Corp (Minneapolis, MN, www.mediject.com), and similar suitable devices Recognized devices comprising a dual vial system include pen-type injector systems to reconstitute a lyophilized drug in a cartridge for application of the reconstituted solution, such as Humatr oPen®. Examples of other suitable devices include prefilled syringes, autoinjectors, needleless injectors and needleless IV infusion sets.

[000113] The presently claimed products include packaging material. The packaging material presents, in addition to the information required by Organs inspection bodies, the conditions under which the product can be used. The packaging material of the present invention provides instructions for the patient to reconstitute at least one protein scaffold in the aqueous diluent to form a solution, and to use said solution over a period of 2 to 24 hours or longer for the product. with two bottles of wet/dry contents. For the single bottle product containing a solution, the label indicates that this solution can be used over a period of 2 to 24 hours or longer. The presently claimed products are useful for use in pharmaceuticals intended for humans.

[000114] The formulations of the present invention can be prepared by a process that comprises mixing at least one protein scaffold and a selected buffer, preferably a phosphate buffer containing saline or a chosen salt. The mixing of at least one protein scaffold and buffer in an aqueous diluent is accomplished using conventional dissolution and mixing procedures. To prepare a suitable formulation, for example, a measured amount of at least one scaffold of protein in water or buffer is combined with the desired buffering agent in water, in amounts sufficient to provide the protein and buffer at the desired concentrations. Variations of this process will be recognized by one of skill in the art. For example, the order in which the components are added, the use of additional additives, and the temperature and pH at which the formulation is prepared are factors that can be optimized for the concentration and means of administration used.

[000115] The claimed stable or preserved formulations may be provided to patients in the form of clear solutions or in the form of double vials comprising a lyophilized protein scaffold vial which is reconstituted with a second vial containing a preservative or buffer and excipients in an aqueous diluent. Either a single vial of solution, or a double vial that requires reconstitution, can be reused multiple times and may be sufficient for a single cycle or multiple cycles of the patient's treatment and thus provide a more convenient treatment regimen than the currently available.

[000116] Other formulations or other methods for stabilizing the protein scaffold may result in a not necessarily clear solution of lyophilized powder comprising the protein scaffold. Among the non-clear solutions are formulations that comprise suspensions of particulates, said particulates consisting of a composition containing the protein scaffold in a structure of variable and known dimension, among others, as a microsphere, microparticle, nanoparticle, nanosphere or liposome. Such relatively homogeneous formulations of essentially spherical particulate matter containing an active agent can be formed by placing an aqueous phase containing the active agent and a polymer in contact with a non-aqueous phase, followed by evaporating the non-aqueous phase to cause coalescence of particles of the active agent. aqueous phase, as disclosed in US No. 4,589,330. Porous microparticles can be prepared using a first phase containing active agent and a polymer dispersed in a continuous solvent, and removing said solvent from the suspension by freeze-drying or dilution-extraction-precipitation, as shown in US No. 4,818,542. Preferred polymers for these preparations are natural or synthetic copolymers or polymers selected from the group consisting of gelatin, agar, starch, arabinogalactan, albumin, collagen, polyglycolic acid, polylactic acid, glycolide-L(-) lactide poly(epsilon-caprolactone, poly(epsilon-caprolactone-CO-lactic acid), poly(epsilon-caprolactone-CO-glycolic acid), poly(β-hydroxybutyric acid), polyethylene oxide, polyethylene, poly(alkyl-2-cyanoacrylate), poly( hydroxyethyl methacrylate), polyamides, poly(amino acids), poly(2-hydroxyethyl DL-aspartame), poly(urea ester), poly(L-phenylalanine/ethylene glycol/1,6-diisocyanate hexane) and poly( methyl methacrylate.) Particularly preferred polymers are polyesters, such as polyglycolic acid, polylactic acid, glycolide-L(-) lactide, poly(epsilon-caprolactone, poly(epsilon-caprolactone-CO-lactic acid) and poly(epsilon-caprolactone acid) -CO-glycolic. Solvents useful for dissolving the polymer and/or acetyl These include: water, hexafluoroisopropanol, methylene chloride, tetrahydrofuran, hexane, benzene, or hexafluoroacetone sesquihydrate. The process of dispersing the phase-containing active with a second phase may include pressure to force said first phase through an orifice in a nozzle to affect droplet formation.

[000117] Dry powder formulations may result from processes other than lyophilization, such as spray drying or solvent extraction by evaporation or precipitation of a crystalline composition, followed by one or more steps to remove the aqueous or non-aqueous solvent. The preparation of a spray dried protein scaffold composition is disclosed in U.S. No. 6,019,968. Protein scaffold compositions in dry powder form can be produced by spray drying solutions or slurries of the protein scaffold and, optionally, excipients, in a solvent under conditions to obtain a dry, respirable powder. Solvents can include polar compounds, such as water and ethanol, which can be readily dried. The stability of the protein framework can be optimized by performing spray drying procedures in the absence of oxygen, such as under a blanket of nitrogen, or by using nitrogen as the drying gas. Another relatively dry formulation is a dispersion of a plurality of perforated microstructures dispersed in a suspending medium that typically comprises a hydrofluoroalkane propellant as disclosed in WO 9916419. The stabilized dispersions can be delivered to a patient's lungs using a metered dose inhaler. Equipment useful in the commercial manufacture of spray drying drugs is produced by Buchi Ltd. or Niro Corp.

[000118] The at least one protein scaffold, either in the stable or preserved formulations, or in the solutions described herein, can be administered to a patient in accordance with the present invention by a variety of application methods, including subcutaneous injection. or intramuscular, transdermal, pulmonary, transmucosal, implant, osmotic pump, cartridge, micropump or other means known to those skilled in the art, as is well known in the art.

Therapeutic Applications

[000119] The present invention also provides a method for modulating or treating a disease, in a cell, tissue, organ, animal or patient, as known in the art or as described in the present invention, using at least one protein scaffold of the present invention, for example by administering a therapeutically effective amount of the protein scaffold to, or contacting the same with, the cell, tissue, organ, animal or patient . The present invention also provides a method for modulating or treating a disease in a cell, tissue, organ, animal or patient including, but not limited to, at least one of obesity, an immunological disease, a cardiovascular disease, an infectious disease, a malignant disease or a neurological disease.

[000120] The present invention also provides a method for modulating or treating at least one immunological disease in a cell, tissue, organ, animal or patient including, but not limited to, at least one of arthritis rheumatoid arthritis, juvenile rheumatoid arthritis, systemic onset juvenile rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, gastric ulcer, seronegative arthropathies, osteoarthritis, osteolysis, aseptic loosening of orthopedic implants, inflammatory bowel disease, ulcerative colitis, systemic lupus erythematous, antiphospholipid syndrome, iridocyclitis/ uveitis/optic neuritis, idiopathic pulmonary fibrosis, systemic vasculitis/Wegener's granulomatosis, sarcoidosis, orchitis/vasectomy reversal procedures, allergic/atopic diseases, asthma, allergic rhinitis, eczema, allergic contact dermatitis, allergic conjunctivitis, pneumonia hypersensitivity, transplants, organ transplant rejection, v-graft disease ersus-host, systemic inflammatory response syndrome, sepsis syndrome, gram-positive sepsis, gram-negative sepsis, culture-negative sepsis, fungal sepsis, neutropenic fever, urosepsis, meningococcemia, trauma/hemorrhage, burns, radiation exposure ionizing disease, acute pancreatitis, respiratory distress syndrome in adults, rheumatoid arthritis, alcohol-induced hepatitis, chronic inflammatory conditions, sarcoidosis, Crohn's pathology, sickle cell anemia, diabetes, nephrosis, atopic diseases, hypersensitivity reactions, allergic rhinitis, hay fever , perennial rhinitis, conjunctivitis, endometriosis, asthma, urticaria, systemic anaphylaxis, dermatitis, pernicious anemia, hemolytic disease, thrombocytopenia, graft rejection of any organ or tissue, kidney transplant rejection, heart transplant rejection, heart transplant rejection liver, pancreas transplant rejection, lung transplant rejection, bone marrow transplant (BMT) rejection , skin allograft rejection, cartilage transplant rejection, bone graft rejection, small bowel transplant rejection, fetal thymus implant rejection, parathyroid transplant rejection, xenograft rejection of any organ or tissue, allograft rejection , anti-receptor hypersensitivity reactions, Graves' disease, Raynaud's disease, insulin-resistant type B diabetes, asthma, myasthenia gravis, antibody-mediated cytotoxicity, type III hypersensitivity reactions, POEMS syndrome (polyneuropathy syndrome, organomegaly, endocrinopathy, gammopathy monoclonal and skin changes), polyneuropathy syndrome, organomegaly, endocrinopathy, monoclonal gammopathy, skin changes, antiphospholipid syndrome, pemphigus, scleroderma, mixed connective tissue disease, idiopathic Addison's disease, diabetes mellitus, chronic active hepatitis, primary biliary cirrhosis , vitiligo, vasculitis, post-MI cardiotomy syndrome, type IV hypersensitivity, d contact hermatitis, hypersensitivity pneumonitis, allograft rejection, granulomas due to intracellular organisms, drug sensitivity, metabolic/idiopathic Wilson's disease, hemochromatosis, alpha-1-antitrypsin deficiency, diabetic retinopathy, Hashimoto's thyroiditis, osteoporosis, evaluation of hypothalamic-pituitary-adrenal axis, primary biliary cirrhosis, thyroiditis, encephalomyelitis, cachexia, cystic fibrosis, neonatal chronic lung disease, chronic obstructive pulmonary disease (COPD), familial hematophagocytic lymphohistiocytosis, skin problems, psoriasis, alopecia, nephrotic syndrome, nephritis, nephritis glomerular, acute renal failure, hemodialysis, uremia, pre-eclampsia toxicity, okt3 therapy, anti-cd3 therapy, cytokine therapy, chemotherapy, radiation therapy (eg, including, but not limited to, asthenia, anemia, cachexia, and the like ), chronic salicylate poisoning, and the like. See, for example, the Merck Manual, 12th to 17th Editions, Merck & Company, Rahway, NJ, USA (1972, 1977, 1982, 1987, 1992, 1999), and Pharmacotherapy Handbook, Wells et al., Publishers, Second Edition, Appleton and Lange, Stamford, CT, USA (1998, 2000), each of which is incorporated herein by reference in its entirety.

[000121] The present invention also provides a method for modulating or treating at least one cardiovascular disease in a cell, tissue, organ, animal or patient including, but not limited to, at least one of a syndrome cardiac stunning, myocardial infarction, congestive heart failure, stroke, ischemic stroke, hemorrhage, acute coronary syndrome, arteriosclerosis, atherosclerosis, restenosis, diabetic arteriosclerotic disease, hypertension, arterial hypertension, renovascular hypertension, syncope, shock, syphilis of the cardiovascular system, heart failure, cor pulmonale, primary pulmonary hypertension, cardiac arrhythmias, atrial ectopic beats, atrial flutter, atrial fibrillation (prolonged or paroxysmal), post-perfusion syndrome, inflammatory response to cardiopulmonary revascularization, chaotic or multifocal atrial tachycardia, regular narrow QRS tachycardia, specific arrhythmias s, ventricular fibrillation, His bundle arrhythmias, atrioventricular block, branch bundle block, myocardial ischemic disorders, coronary artery disease, angina pectoris, myocardial infarction, cardiomyopathy, dilated congestive cardiomyopathy, restrictive cardiomyopathy, valvular heart disease, endocarditis , pericardial disease, cardiac tumors, aortic and peripheral aneurysms, aortic dissection, aortic inflammation, occlusion of the abdominal aorta and its ramifications, peripheral vascular disorders, arterial occlusive disorders, peripheral atherosclerotic disease, thromboangiitis obliterans, functional peripheral arterial disorders, phenomenon and Raynaud's disease, acrocyanosis, erythromelalgia, venous diseases, venous thrombosis, varicose veins, arteriovenous fistula, lymphedema, lipedema, unstable angina, reperfusion injury, post-pumping syndrome, ischemia-reperfusion injury, and the like. Such a method may optionally comprise administering an effective amount of a composition or pharmaceutical composition comprising at least one protein scaffold to a cell, tissue, organ, animal or patient in need of such modulation, treatment or therapy. .

[000122] The present invention also provides a method for modulating or treating at least one infectious disease in a cell, tissue, organ, animal or patient, including, but not limited to, at least one of : acute or chronic bacterial infection, acute or chronic parasitic or infectious processes, including bacterial, viral and fungal infections, HIV infection/HIV neuropathy, meningitis, hepatitis (e.g. A, B or C, or similar), septic arthritis , peritonitis, pneumonia, epiglottitis, E. coli 0157:h7, hemolytic uremic syndrome/thrombolytic thrombocytopenic purpura, malaria, dengue hemorrhagic fever, leishmaniasis, leprosy, toxic shock syndrome, streptococcal myositis, gas gangrene, Mycobacterium tuberculosis, Mycobacterium avium intracellulare, pneumonia Pneumocystis carinii, pelvic inflammatory disease, orchitis/epididymitis, legionella, Lyme disease, influenza A, Epstein-Barr virus, virus-associated hemophagocytic syndrome, encephalitis viral alitis/aseptic meningitis, and the like.

[000123] The present invention also provides a method for modulating or treating at least one malignant disease in a cell, tissue, organ, animal or patient, including, but not limited to, at least one of : leukemia, acute leukemia, acute lymphoblastic leukemia (ALL), acute lymphocytic leukemia, B-cell, T-cell or FAB ALL, acute myeloid leukemia (AML), acute myelogenous leukemia, chronic myelocytic leukemia (CML), chronic lymphocytic leukemia (CLL) , hairy cell leukemia, myelodysplastic syndrome (MDS), lymphoma, Hodgkin's disease, malignant lymphoma, non-Hodgkin's lymphoma, Burkitt's lymphoma, multiple myeloma, Kaposi's sarcoma, colorectal carcinoma, pancreatic carcinoma, nasopharyngeal carcinoma, malignant histiocytosis, syndrome paraneoplastic/hypercalcemia from malignancy, solid tumors, bladder cancer, breast cancer, colorectal cancer, endometrial cancer, head cancer, neck cancer, hereditary non-polypoid cancer, Hodgk's lymphoma in, liver cancer, lung cancer, non-small cell lung cancer, ovarian cancer, pancreatic cancer, prostate cancer, renal cell carcinoma, testicular cancer, adenocarcinomas, sarcomas, malignant melanoma, hemangioma, metastatic disease, bone resorption cancer-related pain, cancer-related bone pain, and the like.

[000124] The present invention also provides a method for modulating or treating at least one neurological disease in a cell, tissue, organ, animal or patient including, but not limited to, at least one of: neurodegenerative diseases, multiple sclerosis, migraine headache, AIDS dementia complex, demyelination diseases such as multiple sclerosis and acute transverse myelitis, extrapyramidal and cerebellar disorders such as corticospinal system lesions, basal ganglia disorders, hyperkinetic movement disorders such as chorea Huntington's disease and senile chorea, drug-induced movement disorders such as those induced by drugs that block CNS dopamine receptors, hypokinetic movement disorders such as Parkinson's disease, progressive supranuclear palsy, structural lesions of the cerebellum, spinocerebellar degenerations such as spinal ataxia, Friedreich's ataxia, cerebellar cortical degenerations lares, multiple system degenerations (Mencel, Dejerine-Thomas, Shi-Drager and Machado-Joseph), systemic disorders (Refsum's disease, abetalipoproteinemia, ataxia, telangiectasia and multi-system mitochondrial disorder), nucleus demyelination disorders, such as multiple sclerosis, acute transverse myelitis, and motor unit disorders such as neurogenic muscle atrophies (horn anterior cell degeneration such as amyotrophic lateral sclerosis, infantile spinal muscular atrophy, and juvenile spinal muscular atrophy), Alzheimer's disease, Down syndrome in the sock -age, diffuse Lewy body disease, Lewy body-related senile dementia, Wernicke-Korsakoff syndrome, chronic alcoholism, Creutzfeldt-Jakob disease, subacute sclerosing panencephalitis, Hallerrorden-Spatz disease, dementia pugilistica, neurotraumatic injury (e.g. spinal cord injury, brain injury, concussion, repetitive concussion), pain, pain of inflammatory origin, autism, depression, stroke, cognitive disorders, epilepsy and the like. Such a method may optionally comprise administering an effective amount of a composition or pharmaceutical composition that comprises at least one TNF variant antibody or specified portion to a cell, tissue, organ, animal or patient in need of such modulation, treatment or therapy. See, for example, the Merck Manual, 16th Edition, Merck & Company, Rahway, NJ, USA (1992).

[000125] The present invention also provides a method for modulating or treating at least one wound, trauma or tissue injury or related chronic problem, in a cell, a tissue, an organ, an animal or a patient including, but not limited to at least one of: physical injury or trauma associated with oral surgery, including periodontal surgery, tooth extraction, endodontic treatment, insertion of dental implants, application and use of dentures, or where the wound is selected of the group consisting of aseptic wounds, blunt wounds, incision wounds, laceration wounds, non-penetrating wounds, open wounds, penetrating wounds, puncture wounds, puncture wounds, septic wounds, infarcts and subcutaneous wounds, or where the wound is selected from the group consisting of ischemic ulcers, pressure ulcers, fistulas, severe bites, thermal burns, and donor site wounds, or where the wound is an injury to phthosa, a traumatic wound, or a herpes-associated lesion.

[000126] Wounds and/or ulcers are commonly found protruding from the skin or onto a mucosal surface, or as a result of an organ infarction ("stroke"). A wound can be the result of a soft tissue defect, an injury, or an underlying condition. In the present context, the term "skin" refers to the outermost surface of the body of an animal, including a human, and encompasses intact or nearly intact skin as well as a surface of skin that is injured. The term "mucosa" refers to the intact or damaged mucosa of an animal, such as a human, and may be oral, buccal, aural, nasal, pulmonary, ocular, gastrointestinal, vaginal, or rectal mucosa.

[000127] In the present context, the term "wound" denotes a bodily injury with disruption of the normal integrity of tissue structures. The term is also intended to encompass the terms "sore", "lesion", "necrosis" and "ulcer". Usually, the term "wound" is a popular term for almost any lesion of the skin or mucous membranes, while the term "ulcer" is a local defect, or an excavation, of the surface of an organ or tissue, which is produced by the elimination of necrotic tissue. The term "injury" generally refers to any tissue defect. Necrosis is related to dead tissue resulting from infection, injury, inflammation, or infarctions.

[000128] The term "wound", used in the present context, denotes any wound (see below for a classification of wounds) and at any specific stage in the healing process, including the stage before any healing has begun, or even before of a specific wound, such as a surgical incision, has been made (prophylactic treatment). Examples of wounds that can be prevented and/or treated in accordance with the present invention are, for example, aseptic wounds, contusion wounds, incision wounds, laceration wounds, non-penetrating wounds (i.e. wounds in which there is no skin disorder but damage to underlying structures), open wounds, penetrating wounds, puncture wounds, puncture wounds, septic wounds, subcutaneous wounds, etc. Examples of decubitus ulcers, mouth ulcers, chromium ulcers, canker sores, pressure ulcers, etc. Examples of ulcers are, for example, peptic ulcer, duodenal ulcer, gastric ulcer, gouty ulcer, diabetic ulcer, ischemic hypertension ulcer, stasis ulcer, ulcus cruris (venous ulcer), sublingual ulcer, submucosal ulcer, symptomatic ulcer, ulcer trophic ulcer, tropical ulcer and venereal ulcer, eg caused by gonorrhea (including urethritis, endocervicitis and proctitis). Conditions related to wounds or ulcers that can be properly treated in accordance with the present invention are burns, anthrax, tetanus, gas gangrene, scarlet fever, erysipelas, sycosis barbae, folliculitis, impetigo contagious or impetigo bullous, etc. There is often some overlap between the use of the terms "wound" and "ulcer" and the terms "wound" and "lesion" and, in addition, the terms are often used at random. Accordingly, as mentioned above, in the present context the term "wound" encompasses the terms "ulcer", "lesion", "sore" and "infarction", these terms being used indiscriminately, unless otherwise indicated.

[000129] The types of wounds to be treated according to the invention also include (i) wounds in general, such as surgical, traumatic, infectious, ischemic, thermal, chemical and bullous wounds, (ii) wounds specific to the oral cavity, such as post-extraction wounds, endodontic wounds especially in connection with the treatment of cysts and abscesses, ulcers and lesions of bacterial, viral or autoimmune origin, mechanical, chemical, thermal, infectious and lichenoid wounds, including herpetic ulcers, aphthous stomatitis, ulcerative gingivitis acute necrotizing disease and burning mouth syndrome are specific examples, and (iii) wounds on the skin such as neoplasm, burns (eg chemical or thermal), injuries (bacterial, viral, autoimmune), bites and surgical incisions. Another way of classifying wounds is: (i) minor tissue loss due to surgical incisions, minor abrasions and minor bites, or (ii) significant tissue loss. The latter group includes ischemic ulcers, pressure ulcers, fistulas, lacerations, severe bites, thermal burns, and donor site wounds (soft and hard tissue), as well as infarctions.

[000130] Other wounds that are of importance in connection with the present invention are wounds such as ischemic ulcers, pressure ulcers, fistulas, severe bites, thermal burns and donor site wounds. Ischemic ulcers and pressure ulcers are wounds that normally only heal very slowly, and especially in these cases, an improved and faster healing process is clearly of great importance to the patient. Furthermore, the costs involved in treating patients suffering from these wounds are markedly reduced when healing is optimized and occurs faster.

[000131] Donor site wounds are those which, for example, occur in connection with the removal of hard tissues from one part of the body to another, for example in connection with transplants. The wounds resulting from these operations are very painful and optimal healing is therefore extremely valuable. The term "skin" is used in a very broad sense, encompassing the epidermal layer of the skin and — in cases where the surface of the skin is more or less injured — also the dermal layer of the skin. In addition to the stratum corneum, the epidermal layer of the skin is the outer (epithelial) layer, and the connective tissue layer of the skin is called the dermis.

[000132] Any method of the present invention may comprise administering an effective amount of a composition or pharmaceutical composition comprising at least one protein scaffold to a cell, tissue, organ, animal or patient in need of such modulation, treatment or therapy. That method may optionally further comprise co-administration or combination therapy for treating those diseases or disorders, wherein the administration of said at least one protein scaffold, or the specific portion or variant thereof, further comprises the prior, simultaneous and/or subsequent administration of at least one selected from at least one TNF antagonist (for example, but not limited to, a chemical or protein antagonist of TNF, a monoclonal or polyclonal antibody to TNF or a fragment of the same, a receptor for soluble TNF (e.g. p55, p70 or p85) or a fragment thereof, fusion polypeptides thereof, or a small molecule TNF antagonist, e.g. a TNF-binding protein I or II ( TBP-1 or TBP-II), nerelimomab, infliximab, etanercept (Enbrel™), adalimumab (Humira™), CDP-571, CDP-870, afelimomab, lenercept and the like), an antirheumatic (e.g., methotrexate, auranofin, aurothioglycol se, azathioprine, gold sodium thiomalate, hydroxy chloroquine sulfate, leflunomide, sulfasalazine), a muscle relaxant, a narcotic, a non-steroidal anti-inflammatory drug (NSAID), an analgesic, an anesthetic, a sedative, a local anesthetic , a neuromuscular blocker, a microbicide (e.g., an aminoglycoside, an antifungal, an antiparasitic, an antiviral, a carbapenem, a cephalosporin, a fluoroquinolone, a macrolide, a penicillin, a sulfonamide, a tetracycline, or other microbicide), a antipsoriatic, a corticosteroid, an anabolic steroid, a diabetes-related agent, a mineral, a nutritional, a thyroid agent, a vitamin, a calcium-related hormone, an antidiarrheal, an antitussive, an antiemetic, an antiulcer, a laxative, an anticoagulant, an erythropoietin (e.g. epoetin alfa), a filgrastim (e.g. G-CSF, Neupogen), a sargramostim (GM-CSF, Leukine), an immunization, an immunoglobulin, an immuno suppressor (eg basiliximab, cyclosporine, daclizumab), a growth hormone, a hormone replacement drug, an estrogen receptor modulator, a mydriatic, a cycloplegic, an alkylating agent, an antimetabolite, a mitotic inhibitor, a radiopharmaceutical, an antidepressant, an antimanic agent, an antipsychotic, an anxiolytic, a hypnotic, a sympathomimetic, a stimulant, donepezil, tacrine, an asthma drug, a beta agonist, an inhaled steroid, a leukotriene inhibitor, a methylxanthine, a cromolyn, an epinephrine or analogue thereof, a dornase alfa (Pulmozyme), a cytokine or a cytokine antagonist. Suitable dosages are well known in the art. See, for example, Wells et al., Editors, Pharmacotherapy Handbook, 2nd Edition, Appleton and Lange, Stamford, CT, USA (2000), PDR Pharmacopoeia, Tarascon Pocket Pharmacopoeia 2000, Deluxe Edition, Tarascon Publishing, Loma Linda, CA , USA (2000), Nursing 2001 Handbook of Drugs, 21st Edition, Springhouse Corp., Springhouse, PA, USA, 2001, Health Professional's Drug Guide 2001, Editor, Shannon, Wilson, Stang, Prentice-Hall, Inc, Upper Saddle River , NJ, USA, each of which is incorporated herein by reference in their entirety.

[000133] Cytokines include any known cytokine. See, for example, CopewithCytokines.com. Cytokine antagonists include, but are not limited to, any antibody, protein framework fragment or mimetic, any soluble receptor, fragment or mimetic, any small molecule antagonist, or any combination thereof.

[000134] Typically, treatment of pathological conditions is accomplished by administering an effective amount or dosage of at least one protein scaffold composition that results in a total, on average, in the range of at least about 0.01 to 500 milligrams of at least one scaffold protein per kilogram of patient per dose, and preferably from at least about 0.1 to 100 milligrams of scaffold protein/kilogram of patient for single or multiple administration, depending on the specific activity of the drug active agent contained in the composition. Alternatively, the serum concentration may comprise from 0.1 to 5000 µg/ml of serum concentration by single or multiple administration. Suitable dosages are known to professionals in the medical field and will, of course, depend on the particular disease state, specific activity of the composition administered and the particular patient undergoing treatment. In some cases, to achieve the desired therapeutic amount, it may be necessary to provide repeated administrations, i.e., repeated individual administrations of a particular metered or monitored dosage, where individual administrations are repeated until the desired daily dose or effect is achieved.

[000135] Preferred doses may optionally include from about 0.1 to 99 and/or from 100 to 500 mg/kg/administration, or any range, value, or fraction thereof, or until a serum concentration of about 0.1 to 5,000 μg/ml by single or multiple administration, or any range, value, or fraction thereof. A preferred dosage range for the protein scaffold of the present invention is from about 1 mg/kg, to about 3, about 6, or about 12 mg/kg of patient body weight.

[000136] Alternatively, the dosage administered may vary depending on known factors such as the pharmacodynamic characteristics of the specific agent, and the mode and route of administration thereof, age, health and weight of the recipient, nature and extent of symptoms, type of concomitant treatment, frequency of treatment and desired effect. Typically, a dosage of the active ingredient can be around 0.1 to 100 milligrams per kilogram of body weight. Usually 0.1 to 50 and preferably 0.1 to 10 milligrams per kilogram per administration or in sustained release form is effective to obtain the desired results.

[000137] As a non-limiting example, treatment of humans or animals may be offered as a single or periodic dosage of at least one scaffold protein of the present invention, from about 0.1 to 100 mg/kg or any range, amount or fraction thereof per day, on at least one of days 1 to 40 or, alternatively or additionally, at least one of a week from 1 to 52 or, alternatively or additionally, at least one of days 1 to 20 years, or any combination thereof, using single, infused, or repeated doses.

[000138] Dosage (composition) forms suitable for internal administration generally contain from about 0.001 milligram to about 500 milligrams of active ingredient per unit or container. In such pharmaceutical compositions, the active ingredient will usually be present in an amount of from about 0.5 to 99.999%, by weight, based on the total weight of the composition.

[000139] For parenteral administration, the protein framework may be formulated as a solution, suspension, emulsion, particle, powder or lyophilized powder in association, or supplied separately, with a pharmaceutically acceptable parenteral vehicle. Examples of such vehicles are water, saline, Ringer's solution, dextrose solution and 1 to 10% human serum albumin. Liposomes and non-aqueous vehicles such as fixed oils can also be used. The lyophilized vehicle or powder may contain additives that maintain isotonicity (eg, sodium chloride, mannitol) and chemical stability (eg, buffers and preservatives). The formulation is sterilized by known or suitable techniques.

[000140] Suitable pharmaceutical carriers are described in the most recent edition of Remington's Pharmaceutical Sciences, A. Osol, a standard reference text in the field.

Alternative Administration

[000141] Many developed and known modes can be used in accordance with the present invention to deliver pharmaceutically effective amounts of at least one protein scaffold according to the present invention. While pulmonary administration is used in the following description, other modes of administration can be used in accordance with the present invention, with suitable results. The protein scaffolds of the present invention can be applied to a carrier, in the form of a solution, emulsion, colloid or suspension, or in the form of a dry powder, using any of a variety of devices and methods suitable for administration by inhalation or other modes described herein or known in the art.

Administration and Parenteral Formulations

[000142] Formulations for parenteral administration may contain as common excipients sterile water or saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, hydrogenated naphthalenes and the like. Aqueous or oily suspensions for injection may be prepared using a suitable humidifier or emulsifier and a suspending agent, according to known methods. Agents for injection can be a non-toxic, non-orally administrable diluting agent such as an aqueous solution, a sterile injectable solution, or a suspension in a solvent. As a useful vehicle or solvent, water, Ringer's solution, and isotonic saline, among others, are allowed, and as a common solvent or suspension solvent, a sterile, non-volatile oil can be used. For these purposes, any type of non-volatile oil and fatty acid may be used, including natural, synthetic or semi-synthetic, tri, di or monoglyceride natural, synthetic or semi-synthetic fatty acids or fatty oils. Parenteral administration is known in the art and includes, but is not limited to, conventional means of injection, a pressurized, needleless gas injection device as described in U.S. Patent No. 5,851,198, and a laser piercing device as described. in U.S. Patent No. 5,839,446, incorporated herein by reference, in its entirety.

Alternative Application

[000143] The invention further relates to the administration of at least one protein scaffold by parenteral, subcutaneous, intramuscular, intravenous, intra-articular, intrabronchial, intra-abdominal, intracapsular, intracartilaginous, intracavitary, intracelial, intracerebellar, intracerebroventricular, intracolic, intracervical, intragastric, intrahepatic, intramyocardial, intraosseous, intrapelvic, intrapericardial, intraperitoneal, intrapleural, intraprostatic, intrapulmonary, intrarectal, intrarenal, intraretinal, intraspinal, intrasynovial, intrathoracic, intrauterine, intravesical, intralesional, bolus, vaginal, rectal, buccal, subligual, intranasal or transdermal. The at least one protein scaffold composition may be prepared for parenteral use (subcutaneous, intramuscular or intravenous) or any other administration, particularly in the form of liquid solutions or suspensions; for vaginal or rectal use, administration is particularly in semi-solid forms, for example, but not limited to, creams and suppositories; for buccal or sublingual administration it is, for example, but not limited to, in tablet or capsule form; the intranasal form is, for example, but not limited to, in powder form, nasal drops, aerosols or certain agents; the transdermal form is, but is not limited to, a gel, ointment, lotion, suspension or patch delivery system with chemical enhancers such as dimethyl sulfoxide, both to modify the skin structure and to increase the drug concentration in the transdermal patch (Junginger, et al. In "Drug Permeation Enhancement"; Hsieh, DS, Eds., pp. 59-90 (Marcel Dekker, Inc. New York, USA, 1994, fully incorporated herein by reference), or with oxidizing agents that allow for the application of formulations containing proteins and peptides on the skin (WO 98/53847), or the application of electric fields to create temporary transport pathways, such as electroporation, or to increase the mobility of charged drugs through the skin, such as iontophoresis or ultrasound application, such as sonophoresis (US Patents 4,309,989 and 4,767,402) (the above publications and patents being fully incorporated herein by reference).

Pulmonary/Nasal Administration

[000144] For pulmonary administration, preferably, at least one protein scaffold composition is applied in a particle size effective to target the lower airways of the lungs or the sinuses. In accordance with the present invention, at least one protein scaffold may be delivered via any of a variety of inhalation or nasal devices known in the art for the administration of a therapeutic agent by inhalation. Such devices capable of depositing aerosolized formulations into the sinus cavity or alveoli of a patient include metered dosage of inhalers, nebulizers, dry powder generators, sprinklers and the like. Other devices suitable for directing the pulmonary or nasal administration of protein scaffolds are also known in the art. All of these devices can use formulations suitable for administration and delivery of scaffold protein in an aerosol. Such aerosols may consist of any of solutions (aqueous and non-aqueous) or solid particles.

[000145] Metered dose inhalers such as Ventolin® typically use a propellant gas and require actuation during inspiration (See eg WO 94/16970, WO 98/35888). Dry powder inhalers such as Turbuhaler™ (Astra), Rotahaler® (Glaxo), Diskus® (Glaxo), the Spiros™ inhaler (Dura), devices marketed by Inhale Therapeutics, and the Spinhaler® powder inhaler (Fisons) , use actuation by breathing a mixed powder (US 4668218 Astra, EP 237507 Astra, WO 97/25086Glaxo, WO 94/08552 Dura, US 5458135 Inhale, WO 94/06498 Fisons, incorporated herein by reference in their entirety) . Nebulizers such as AERx™ (Aradigm), Ultravent® (Mallinckrodt), and Acorn II® (Marquest Medical Products) (US 5404871 Aradigm, WO 97/22376, the above references being incorporated herein by reference in their entirety), produce aerosols from solutions, while metered dose inhalers and dry powder inhalers, among others, generate small particle aerosols. These specific examples of commercially available inhalation devices are intended to represent the specific devices suitable for the practice of this invention, not to limit the scope of this invention.

[000146] Preferably, a composition comprising at least one protein scaffold is delivered by a dry powder inhaler or a sprinkler. There are several desirable features in an inhalation device for administering at least one protein scaffold of the present invention. For example, delivery by an inhalation device is advantageously reliable, reproducible and accurate. The inhalation device may optionally deliver small dry particles, for example smaller than about 10 µm, preferably about 1 to 5 µm, to provide good breathability.

Administration of protein scaffold compositions in the form of a spray

[000147] A spray comprising the protein scaffold composition may be produced by forcing a suspension or solution containing at least one protein scaffold to pass through a nozzle under pressure. Nozzle size and configuration, applied pressure and liquid feed rate can be chosen to achieve the desired output and particle size. An electrical spray can be produced, for example, by an electric field in connection with a device for feeding a capillary or nozzle. Advantageously, the particles of at least one protein scaffold composition released by a sprinkler have a size of less than about 10 μm, preferably in the range of about 1 μm to about 5 μm, and most preferably of about from 2 μm to about 3 μm.

[000148] Formulations of at least one protein framework composition suitable for use with a sprinkler typically include the protein framework composition in an aqueous solution at a concentration of from about 0.1 mg to about 100 mg of the at least one protein scaffold composition per ml of solution, or mg/g, or any range, value, or fraction thereof. The formulation may include agents such as an excipient, a buffer, an isotonicity agent, a preservative, a surfactant, and preferably zinc. The formulation may also include an excipient or agent for stabilizing the protein scaffold composition, such as a buffer, a reducing agent, a crude protein, or a carbohydrate. Crude proteins useful in formulating protein scaffold compositions include albumin, protamine or the like. Typical carbohydrates useful for formulating protein scaffold compositions include sucrose, mannitol, lactose, trehalose, glucose or the like. The formulation of the protein scaffold composition may also include a surfactant which can reduce or prevent surface-induced aggregation of the protein scaffold composition caused by atomization of the solution in forming an aerosol. Various conventional surfactants can be used, such as fatty acid esters and polyoxy ethylene alcohols, and fatty acid esters of polyoxy ethylene sorbitol. The amounts will generally be in the range of between 0.001 and 14% by weight of the formulation. Especially preferred surfactants for purposes of this invention are polyoxyethylene sorbitan monooleate, polysorbate 80, polysorbate 20 or the like. Additional agents known in the art for formulating a protein, such as protein scaffolds, or specific portions or variants thereof, may also be included in the formulation.

Administration of protein scaffold compositions via nebulizer

[000149] The protein scaffold compositions of the present invention may be administered by a nebulizer such as a jet nebulizer or an ultrasonic nebulizer. Typically, in a jet fogger, a source of compressed air is used to create a high-velocity jet of air through an orifice. As the gas expands beyond the nozzle, a region of low pressure is created which draws a solution of the protein scaffold composition through a capillary tube connected to a reservoir of liquid. The liquid stream from the capillary tube is divided into droplets and unstable filaments as it leaves the tube, creating an aerosol. A variety of configurations, flow rates and deflector types can be used to obtain the desired performance characteristics from a given spray nebulizer. In an ultrasonic nebulizer, high frequency electrical energy is used to create vibrational mechanical energy, typically employing a piezoelectric transducer. This energy is transmitted to the protein scaffold composition formulation, either directly or through a coupling fluid, creating an aerosol that includes the protein scaffold composition. Advantageously, the particles of the protein scaffold composition released by a nebulizer have a size of less than about 10 μm, preferably in the range of about 1 μm to about 5 μm, and most preferably of about 2 μm. at about 3 μm.

[000150] Formulations of at least one protein scaffold suitable for use with a nebulizer, whether jet or ultrasonic, typically include a concentration of from about 0.1 mg to about 100 mg of at least one scaffold of protein. protein per ml of solution. The formulation may include agents such as an excipient, a buffer, an isotonicity agent, a preservative, a surfactant, and preferably zinc. The formulation may also include an excipient or agent for stabilizing the at least one protein scaffold composition, such as a buffer, a reducing agent, a crude protein, or a carbohydrate. Crude proteins useful in at least one formulation of protein scaffold compositions include albumin, protamine or the like. Typical carbohydrates useful for formulating at least one protein scaffold include sucrose, mannitol, lactose, trehalose, glucose or the like. The formulation of the at least one protein scaffold may also include a surfactant that can reduce or prevent surface-induced aggregation of the at least one protein scaffold caused by atomization of the solution in forming an aerosol. Various conventional surfactants can be used, such as fatty acid esters and polyoxyethylene alcohols, and polyoxyethylene sorbitan fatty acid esters. The amounts will generally be in the range of about 0.001 to 4%, by weight of the formulation. Especially preferred surfactants for purposes of this invention are polyoxyethylene sorbitan monooleate, polysorbate 80, polysorbate 20 or the like. Additional agents known in the art for formulating a protein, such as a protein scaffold, may also be included in the formulation.

Administration of protein framework compositions by means of a metered dose inhaler

[000151] In a metered dose inhaler (MDI), a propellant, at least one protein scaffold, and any excipients or other additives are contained in a tube in the form of a mixture that includes a liquefied compressed gas. Actuation of the metering valve releases the mixture in the form of an aerosol, preferably containing particles in a size range of less than about 10 μm, preferably from about 1 μm to about 5 μm, and most preferably , from about 2 μm to about 3 μm. The desirable aerosol particle size can be obtained using a formulation of the protein scaffold composition produced by various methods known to those skilled in the art, including jet milling, spray drying, critical point condensation, or the like. Preferred metered dose inhalers include those manufactured by 3M or Glaxo and which employ a hydrofluorocarbon propellant. Formulations of at least one protein scaffold for use with a metered dose inhaler device will generally include a finely divided powder containing at least one protein scaffold in the form of a suspension in a non-aqueous medium, for example , suspended in a propellant with the aid of a surfactant. The propellant may be any conventional material employed for this purpose, such as a chlorofluorocarbon, a hydrochlorofluorocarbon, a hydrofluorocarbon or a hydrocarbon, which includes trichlorofluoromethane, dichlorodifluoromethane, dichlorotetrafluoroethanol and 1,1,1,2-tetrafluoroethane, HFA-134a (hydrofluoroalkane- 134a), HFA-227 (hydrofluoroalkane-227) or the like. Preferably, the propellant is a hydrofluorocarbon. The surfactant may be chosen to stabilize at least one protein scaffold in the form of a suspension in the propellant, to protect the active agent from chemical degradation and the like. Suitable surfactants include sorbitan trioleate, soy lecithin, oleic acid or the like. In some cases, solution aerosols using solvents such as ethanol are preferred. Additional agents known in the art for formulating a protein may also be included in the formulation. One skilled in the art will recognize that the methods of the present invention can be carried out by administering at least one protein scaffold composition to the lungs by means of devices not described herein.

Administration and Formulations for Oral Use

[000152] Formulations for oral administration rely on co-administration of adjuvants (e.g. resorcinols and non-ionic surfactants such as polyoxyethylene oleyl ether and n-hexadecyl polyethylene ether) to artificially increase the permeability of intestinal walls as well as co-administration of enzyme inhibitors (eg, pancreatic trypsin inhibitors, diisopropyl fluorophosphate (DFF) and trasylol) to inhibit enzymatic degradation. Formulations for the application of hydrophilic agents that include proteins and protein scaffolds, as well as a combination of at least two surfactants intended for oral, buccal, mucosal, nasal, pulmonary, vaginal, transmembrane or rectal administration, are disclosed in US No. 6,309 .663. The active constituent compound of the solid type dosage form, for oral administration, may be mixed with at least one additive, including sucrose, lactose, cellulose, mannitol, trehalose, raffinose, maltitol, dextran, starches, agar, arginates, chitins, chitosans, pectins, gum tragacanth, gum arabic, gelatin, collagen, casein, albumin, synthetic or semi-synthetic polymer, and glyceride. Such dosage forms may also contain other types of additives, for example, inactive diluting agent, lubricants such as magnesium stearate, paraben, preservative agent such as sorbic acid, ascorbic acid, alpha-tocopherol, antioxidants such as cysteine, disintegrator , binder, thickener, buffering agent, sweetening agent, flavoring agent, perfuming agent, etc.

[000153] Tablets and pills can be further processed into enteric coated preparations. Liquid preparations for oral administration include emulsion, syrup, elixir, suspension and solution preparations permitted for medical use. Such preparations may contain inactive diluting agents commonly used in said field, for example water. Liposomes have also been described as drug delivery systems for insulin and heparin (U.S. Patent No. 4,239,754). More recently, microspheres of artificial polymers of mixed amino acids (proteinoids) have been used to deliver drugs (U.S. Patent No. 4,925,673). Additionally, carrier compounds described in U.S. Patent No. 5,879,681 and U.S. Patent No. 5,871,753, and used for oral application of biologically active agents, are known in the art.

Administration and Mucosal Formulations

[000154] A formulation for oral administration of a bioactive agent encapsulated in one or more excipients based on biocompatible polymers or copolymers, preferably a biodegradable polymer or copolymer, forms microcapsules which, due to their adequate size, result in the fact that the agent reach the aggregated lymph nodes, also known as "Peyer's patch" or "GALT" of the animal, and be absorbed by them, without loss of efficacy due to the agent passing through the gastrointestinal tract. Similar aggregated lymph nodes can be found in the bronchial tubes (BALT) and large intestine. The tissues described above are commonly called mucosa-associated lymphoreticular tissues (MALT). For absorption across mucosal surfaces, compositions and methods of delivering at least one protein scaffold include an emulsion comprising a plurality of particles, a mucoadhesive macromolecule, a bioactive peptide, and a continuous aqueous phase that promotes absorption across mucosal surfaces by obtaining the mucoadhesion of the emulsion particles (US Patent No. 5,514,670). Mucous surfaces suitable for application of the emulsions of the present invention may include corneal, conjunctival, buccal, sublingual, nasal, vaginal, pulmonary, stomach, intestinal and rectal routes of administration. Formulations for vaginal or rectal administration, for example in suppositories, may contain excipients, for example polyalkylene glycols, petroleum jelly, cocoa butter and the like. Formulations for intranasal administration can be solid and contain as excipients, for example, lactose, or can be an aqueous or oily solution of nasal drops. For buccal administration, excipients include sugars, calcium stearate, magnesium stearate, pregelatinized starch, and the like (U.S. Patent No. 5,849,695).

Administration and Transdermal Formulations

[000155] For transdermal administration, the at least one protein scaffold is encapsulated in a delivery device, such as a liposome or polymeric nanoparticles, microparticles, microcapsules, or microspheres (herein collectively called microparticles, unless otherwise specified). A number of suitable devices are known, including microparticles produced from synthetic polymers such as polyhydroxy, acids such as polylactic acid, polyglycolic acid and copolymers thereof, polyorthoesters, polyanhydrides and polyphosphazene, and natural polymers such as collagen, polyamino acids, albumin and other proteins. , alginate and other polysaccharides and combinations thereof (US Patent No. 5,814,599).

Formulations and Prolonged Administration

[000156] It may be desirable to deliver the compounds of the present invention to the subject over extended periods of time, for example over periods of one week to one year, from a single administration. Various slow release, depot or implant dosage forms can be used. For example, a dosage form may contain a non-toxic pharmaceutically acceptable salt of the compounds having a low degree of solubility in body fluids, for example (a) an acid addition salt with a polybasic acid such as phosphoric acid, sulfuric acid, citric acid, tartaric acid, tannic acid, pamoic acid, alginic acid, polyglutamic acid, naphthalene mono or disulfonic acids, polygalacturonic acid and the like, (b) a salt with a polyvalent metal cation such as zinc, calcium, bismuth, barium, magnesium, aluminum, copper, cobalt, nickel, cadmium and the like, or with an organic cation formed from, for example, N,N'-dibenzyl-ethylene diamine or ethylene diamine, or (c) combinations of (a) and (b), for example a zinc tannate salt. Additionally, the compounds of the present invention, or preferably a relatively insoluble salt such as those described above, may be formulated into a gel, for example an aluminum monostearate gel with, for example, sesame oil, suitable for injection. Particularly preferred salts are zinc salts, zinc tannate salts, pamoate salts and the like. Another type of slow release depot formulation for injection could contain the compound or dispersed salt for encapsulation in a slowly degrading, non-antigenic, non-toxic polymer, such as a polylactic acid/polyglycolic acid polymer, for example as described in US Patent No. 3,773,919. Compounds or, preferably, relatively insoluble salts, such as those described above, may also be formulated into silastic cholesterol matrix pellets, particularly for use in animals. Additional slow-release implant or depot formulations, e.g., gas or liquid liposomes, are known in the literature (US Patent No. 5,770,222 and "Sustained and Controlled Release Drug Delivery Systems", JR Robinson ed., Marcel Dekker, Inc., NY, USA, 1978).

[000157] Having described the invention in general, the same will be more readily understood by reference to the following examples, which are provided by way of illustration and are not intended as limiting.

Examples Example 1 - Fibcon Design

[000158] The 10th FN3 domain of human fibronectin (SEQ ID NO: 10) was explored as an alternative scaffold capable of being manipulated to bind to specific target molecules through surface exposed loops structurally analogous to complementarity determining regions of the antibody (CDR), called B:C, D:E, and F:G loops (Figure 1) (Koide, et al., J Mol Biol 284: 1141-51, 1998). The fibronectin protein contains 14 other independently folded FN3 domains, and all of these are predicted to adopt a similar fold to the 10th FN3 domain based on sequence similarity (SEQ ID NO: 1 to 9, 11 to 15). Indeed, structural conservation for several of these domains is confirmed by high-resolution structures of fibronectin FN3 domains 1, 7, 8, 9, 10, 12, 13, and 14 (Vakonakis, et al., Embo J 26: 2575 a 2583, 2007; Leahy, et al., Cell 84: 155 to 164, 1996; Sharma, et al., Embo J 18: 1468-79, 1999). In order to confirm that all 15 domains can form independently folded units, the gene sequences encoding each domain were obtained by PCR amplification from a universal human cDNA source (Biochain Institute Inc. (Hayward, CA, USA)) using standard PCR methods, subcloned into a modified pET15 vector (Novagen), transformed into E. coli BL21Star(DE3) (Invitrogen) and plated on LB agar plates containing 75 μg/ml carbenicillin. Nucleotides encoding a 6X polyhistidine tag were added to the C-terminal end of each gene during the PCR step. The FN3 7 domain cannot be cloned correctly from this source and therefore was not included in the analysis presented here. For each construct, a single colony was selected and grown overnight at 37°C in 50 ml of TB medium containing 2% glucose and 100 μg/ml carbenicillin. This culture was used to seed 500 mL of autoinduction medium (Overnight Express Instant TB medium, Novagen) in a 2.5 L Ultra Yield flask (Thomson Instrument Company). Proliferation and expression were done using a dual program (3 hours at 37°C, 300 rpm, followed by 16 hours at 30°C, 250 rpm) in an ATR Multitron shaking incubator.

[000159] The culture was collected and centrifuged at 7,000 rpm for 15 minutes in a JL8.1 rotor to pellet the cells. Cells were resuspended in 30 ml of buffer containing 20 mM sodium phosphate, pH 7.5, 500 mM NaCl, 10% glycerol, 20 mM imidazole, 0.37 mg/ml lysozyme, 1X Complete Protease inhibitor (EDTA free, Roche) and Benzonase (Sigma-Aldrich, 0.25 μl/ml final), and lysed with a Misonix XL2020 sonicator for 5 minutes on ice in pulse mode (5 seconds on, 30 seconds off). Insoluble material was removed by centrifugation at 17,000 rpm for 30 minutes in a JA-17 rotor.

[000160] FN3 proteins were purified from the soluble lysate in a 2-step chromatographic process. First, the protein was captured by immobilized metal affinity chromatography, adding 2 mL of Ni-NTA agarose microspheres (Qiagen) to the lysate and placing it on a shaking platform for 1 hour at 4°C. The resin was then packed on a Poly-Prep column (Bio-Rad) and washed with 20 mM sodium phosphate, pH 7.5, 500 mM NaCl, 10% glycerol and 20 mM imidazole to remove the unbound material. Proteins were eluted from the resin with 20 mM sodium phosphate, pH 7.5, 500 mM NaCl, 10% glycerol and 500 mM imidazole. Fractions were analyzed by SDS-PAGE with either Coomassie staining or Western blot using HRP-conjugated anti-His antibody (Immunology Consultants Laboratory). The desired fractions were pooled and dialyzed in PBS at pH 7.4. As a second purification step, the protein was loaded onto a Superdex-75 HiLoad 16/60 column (GE Healthcare), equilibrated in PBS. Fractions were analyzed by SDS-PAGE, and those containing the FN3 protein were pooled and concentrated using a Centriprep UltraCel YM-3 concentrator (Amicon).

[000161] Protein concentration was determined using a BioTek plate reader to measure sample absorbance at 280 nm. The final preparation was analyzed by Coomassie staining, Western blot with anti-His antibody, and by HPLC-SEC using a G3000SW-XL column (TOSOH Biosciences) equilibrated in PBS. SDS-PAGE analysis shows that the FN3 domains migrate between 6 and 14 kDa, according to the predicted masses for the monomeric proteins.

[000162] The folding and thermal stability of each FN3 domain was characterized by differential scanning calorimetry. Differential scanning calorimetry data were obtained by heating 1.0 mg/mL solutions of each FN3 domain in PBS from 35°C to 95°C at a rate of 1°C/minute in an N-DSCII calorimeter ( Applied Thermodynamics). A unique buffer curve was subtracted to produce the profiles shown in Figures 2A-N. From these data, melting temperatures were calculated for each domain using the CpCalc (Microcal) program, as shown in table 1. These data demonstrate that each domain is independently folded and that these domains exhibit a wide range of thermal stabilities. .

[000163] A multiple sequence alignment of all 15 fibronectin FN3 domains was produced in order to design a consensus protein sequence. Analysis of the multiple sequence alignment in Figure 3 shows that although these 15 domains fold into similar structures, they have only modest sequence identities, in the range of 27 to 48%. A first consensus sequence was designed by incorporating the most conserved amino acid at each position of the alignment shown in Figure 3. The first consensus sequence has sequence 42 to 62% identical to the 15 FN3 domains of fibronectin with a mean identity of 45%. The amino acid sequence of the first consensus sequence was translated back and a synthetic gene sequence encoding this protein was synthesized by the "overlapping PCR" technique and subcloned into a modified pET15 vector for expression. For expression, this vector was transformed into E. coli BL21-Gold(DE3) host cells (Stratagene) and a single colony was selected and placed in 0.5 mL of 2YT medium containing ampicillin. Expression was induced by the addition of IPTG to a final concentration of 1 mM when the culture reached an O.D.600 of ~0.6. Expression was monitored by SDS-PAGE after 5 hours of expression at 30°C after induction. SDS-PAGE analysis showed no evidence of expression of this protein in E. coli.

[000164] Since the sequence alignment shown in Figure 3 shows that there are several positions for which it is not possible to define a true consensus sequence, an alternative consensus sequence was designed in an attempt to produce a protein that could be expressed in E coli. The second consensus sequence was identical to the first in 79 of 89 positions, resulting in sequence identities in the range of 37 to 63% (mean identity 51%) to the 15 FN3 domains of fibronectin. The amino acid sequence of the second consensus sequence was translated back and this gene sequence was used to produce an expression vector as described for the first consensus sequence. As with the first, the second consensus sequence was not expressed at detectable levels in E. coli.

[000165] Since the first two drawn consensus sequences were not expressed in E. coli, a third approach was followed. In this approach, a sequence alignment of only the most stable FN3 domains was produced in order to maximize the potential to produce a stable consensus protein. Table 1 shows that domains 1, 2, 5, 8, 10, 12, 14, and 15 have melting temperatures greater than 70°C. A multiple sequence alignment of domains 1, 5, 8, 10, 12, 14, and 15 was generated in order to draw a consensus sequence (Figure 4). Domain 2 was excluded from this alignment as structural analysis showed that the N-terminal strand "A" is disordered in this domain (Vakonakis, et al., Embo J 26: 2575-83, 2007). Fibcon (SEQ ID No: 16) was generated by selecting the most frequently used residue at each position of the alignment shown in Figure 4. Fibcon is 40 to 64% identical to the individual domains aligned in Figure 4.

[000166] The Fibcon amino acid sequence was back-translated to produce the gene sequence shown in SEQ ID NO: 17 and subcloned into a modified pET27 vector (Novagen) by ligase-independent cloning methods. This vector was transformed into BL21-GOLD (DE3) cells, which were plated on LB agar plates supplemented with 50 μg/mL kanamycin. A 10 mL culture of 2YT/Kan was inoculated with 1 colony from this plate and grown overnight at 37°C. This overnight culture was used to seed a 500 mL culture of 2YT supplemented with 50 μg/mL kanamycin, which was grown at 37°C until reaching an OD600 ~ 0.6, at which point IPTG was added to 1 mM and the temperature was reduced to 30°C. Cells were collected by centrifugation at 4000 x g, 5 hours after induction. The resulting cell pellet was lysed by adding 5 mL of BugBuster (Novagen) and 1 μL of Benzonase (Novagen) per gram of wet pellet, stirred at room temperature for 30 minutes, at which point the lysate was cleared by centrifugation at 15,000 xg for 30 minutes. The cleared lysate was applied to a 1 mL column of Hitrap HP Ni-NTA (GE Healthcare), and washed with 10 column volumes of PBS pH 7.4, 12.5 mM imidazole. Fibcon was eluted from the column by applying an imidazole gradient from 12.5 mM to 250 mM over 20 column volumes. Fractions were analyzed by SDS-PAGE (Figures 5A and 5B), pooled, and concentrated before being injected onto a superdex 75 16/60 gel filtration column (GE Healthcare) in PBS. From Figures 5A and 5B, it was shown that Fibcon is expressed completely in the soluble fraction of E. coli, is efficiently purified and is present as a single monomeric species.

[000167] Fibcon folding and thermal stability were evaluated by differential scanning calorimetry and intrinsic tryptophan fluorescence. Differential scanning calorimetry data were obtained by heating a 1.0 mg/mL solution of fibcon in PBS from 30°C to 115°C at a rate of 1°C/minute in an N-DSCII calorimeter (Applied Thermodynamics). A unique buffer curve was subtracted to produce the profile shown in Figure 6. The fusion profile is in line with the folded domain and shows that fibcon is a highly stable protein with thermal transitions at 82°C and 105°C. The transition at 105°C is most likely caused by fibcon aggregation at high temperatures as this transition is concentration dependent.

[000168] Fibcon contains only a single tryptophan residue predicted to be buried in the hydrophobic core of the protein by structural analysis of the other FN3 domains. The fluorescence of this tryptophan residue was used to monitor fibcon folding by equilibrating a fibcon solution (10 μM) in buffered solutions of 50 mM sodium phosphate pH 7.0, 150 mM NaCl and guanidine hydrochloride ( Gu-HCl) in a 96-well plate. The Gu-HCl concentration was changed for each plate well from 0 to 6.5 M concentrations in 0.25 M increments. Tryptophan fluorescence was monitored by excitation at 280 nm and emission at 360 nm with the use of a SpectraMax M5 plate reader equipped with a monochromator (Molecular Devices). Figure 7 shows that fibcon is folded at Gu-HCl concentrations below 4 M. Fluorescence of this tryptophan residue by guanidine titration confirms the folding and structure of fibcon.

Benefits

[000169] The fibcon protein has a high thermal stability of 82°C. Based on this high stability, this scaffold molecule is likely susceptible to amino acid substitution in loops or strands and is easy to manufacture, which makes it a valuable alternative scaffold molecule. Mutations that decrease protein stability tend to be better tolerated in the context of a more stable scaffold, and therefore a stability-optimized scaffold is likely to produce more functional, well-folded ligands from a library of scaffold variants. As this new protein is not a protein encoded by the human genome, it may also provide fewer risks related to generating an immune response against native human fibronectin domains when administered to humans for use as a therapeutic molecule or diagnostic tool compared to framework molecules based on the sequence of native fibronectin domains, such as the 10th FN3 domain.

Example 2 - Generation of Fibcon libraries

[000170] Libraries of Fibcon variants can be made using many different methods, depending on the desired complexity and the relative location of the mutations in the molecule. DNA synthesis methods are preferred to create the mutations spread throughout the Fibcon gene. Restriction enzyme cloning can also be used to recombine DNA fragments containing mutations in different regions of the gene. Saturation mutagenesis a small defined region, such as a single Fibcon loop, can be introduced using a degenerate oligonucleotide and oligonucleotide-directed mutagenesis (Kunkel et al., 1987).

[000171] A fibcon library designed to replace the FG loop with 7 to 12 random amino acids was constructed using oligonucleotide-directed mutagenesis. An oligonucleotide is synthesized to incorporate the degenerate nucleotide NNS at positions encoding the FG loop and two flanking nucleotide sequences of 20 to 27 bp of complementarity to the fibcon gene sequence. In this design, all twenty amino acids are capable of representation in the FG loop.

[000172] The template for oligonucleotide-directed mutagenesis is constructed by replacing the coding sequence of the F:G loop with a stem-loop sequence containing an AscI restriction site. This system allows for the elimination of the initial template DNA after mutagenesis by digesting the resulting DNA with AscI before transformation. To purify a single-stranded DNA template for mutagenesis, a single colony of E. coli CJ236 carrying the vector is selected and added to 5 mL of 2YT growth medium with carbenicillin (50 µg/ml final concentration) and chloramphenicol (10 µg/ml). After 6 hours, helper phage VCSM13 is added to a final concentration of 1010 PFU/ml, and incubated without shaking for 10 minutes, before being transferred to 150 ml of 2YT with carbenicillin (10 µg/ml) and uridine (0. 25 µg/ml) and incubated at 37°C with shaking at 200 rpm overnight. Cells are pelleted by centrifugation, the supernatant collected and the phage pelleted with PEG NaCl. Single-stranded DNA is purified from this pellet using a QIAprep Spin M13 kit (Qiagen) according to the manufacturer's instructions.

[000173] To anneale the degenerate oligonucleotide to the template, 5 μg of the template DNA was combined with oligo at a 10:1 molar ratio in Tris-HCl (50 mM, pH 7.5) and MgCl2 (10 mM) with incubation at 90°C for 2 minutes, 60°C for 3 minutes, and 20°C for 5 minutes. After the annealing reaction, ATP (10 mM), dNTPs (25 mM each), DTT (100 mM), T4 ligase (7 units) and T7 DNA polymerase (10 units) are added to the reaction mixture, with incubation at 14 °C for 6 hours, followed by 20 °C for 12 hours. The resulting DNA is purified using a PCR purification kit (Qiagen), and recovered in 100 μL of water. Library DNA is digested with 10 units of AscI for 4 hours and then purified again with Qiagen's PCR purification kit. The final library DNA is recovered in 50 μL of water. The resulting double-stranded DNA product is then transformed into E. coli MC1061F' by electroporation.

[000174] The transformants are collected in 20 ml of SOC medium, and allowed to recover for 1 hour at 37°C. At the end of the recovery, an aliquot of the transformation is submitted to serial dilution and applied on plates with carbenicillin (100 ug/ml) containing 1% glucose to evaluate the total number of transformants. The remainder of the SOC culture is then used to inoculate 1 L of 2xYT medium with carbenicillin and 1% glucose and grown until the OD600 reaches 0.6. 100 ml of this culture is inoculated with M13 helper phage at 1010/ml and incubated at 37°C before centrifugation. The resulting cell pellet is resuspended in 500 ml of unused 2xYT medium containing carbenicillin (100 µg/ml) and kanamycin (35 µg/ml) and cultured at 30°C overnight before centrifugation. Phage particles are precipitated by the addition of PEG/NaCl and stored at -80°C.

[000175] A second library is designed to simultaneously introduce diversity into fibcon's B:C and F:G loops. For this, two oligonucleotides are synthesized. The forward oligo is phosphorylated and contains the NNS degenerate codon at each position encoding the B:C loop, while the reverse oligo is biotinylated at the 5' end and contains 21 NNS codon bases at each position encoding the F:G loop. Both oligonucleotides are flanked by two 18 bp nucleotide sequences identical to the region preceding and following the region to be mutagenized.

[000176] To construct the library, sixteen 100 μL PCR reactions were performed using the t oligos to amplify the fibcon DNA template, introducing NNS codons into the B:C and F:G loops simultaneously in the process. The double stranded PCR product is mixed with streptavidin magnetic beads (Dynal) in B&W buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.1% Tween-20 ) and incubated for 20 minutes, pulled down with a magnet and washed twice with B&W buffer. The straight filament is eluted from the microspheres with 300 μL of 150 mM NaOH. This "megaprimer", a mixture of long primers over 8 x 10 16 in theoretical diversity, is used for annealing to a single-stranded library template. Building the library is performed as described above for the first library.

Example 3 - Selection of target protein ligands

[000177] In order to make selections of elements from the fibcon library that bind to the target protein, the target protein is biotinylated using sulfo-NHS-LC-biotin (Pierce) prior to dialysis in PBS. For selections, 200 µL of phage displaying libraries are blocked with 200 µL of chemical blocker prior to the addition of biotinylated target protein at concentrations of 500 nM (cycle 1) or 100 nM (cycles 2 and 3). Bound phage are recovered by neutrovidin magnetic beads (Seradyne) in cycle 1, or with streptavidin magnetic beads (Promega) in cycles 2 and 3. Unbound phage are washed off the beads using 5 to 10 washes with 1 mL of Tween Buffered Tris Saline (TBST), followed by two 1 mL washes with Tris Buffered Saline (TBS). Bound phage are eluted from the microspheres by the addition of E. coli MC1061F' in mid-log phase. Infected cells are placed on LB agar plates supplemented with carbenicillin and glucose. The next day, cells are scraped off the plate and grown to mid-log phase, before retrieval with VCSM13 helper phage and overnight cultivation. Phage particles isolated by PEG/NaCl precipitation are used for the next round of selections.

[000178] After 3 or more cycles of panning against the target protein, the result is subcloned into a pET27 vector modified to include a ligase-independent cloning site by PCR amplification of the fibcon gene. This PCR product is annealed to the vector and transformed into BL21-GOLD(DE3) cells (Stratagene). Individual colonies are collected in 1 mL cultures in 96-well plates deep (Corning) and grown to saturation overnight at 37°C. The next day, 50 μL of the overnight culture is used to inoculate a 1 mL unused culture. Cultures are grown at 37°C for 2 hours before adding 1 mM IPTG and reducing the temperature to 30°C. Cells are collected by centrifugation 16 hours after induction, and lysed with 100 µL of BugBuster (Novagen). The resulting lysates are clarified by centrifugation and used to test for IgG binding by ELISA.

[000179] Maxisorp plates (Nunc) are coated with 0.1 µg of anti-HIS antibodies (Qiagen), left overnight, washed with TBST and blocked with Starting Block T20 (Thermo Scientific). The clarified lysates diluted 1:4 in Starting Block are added to the plates and allowed to bind for 1 hour before washing with TBST. Biotinylated IgG or biotinylated HSA is added at a concentration of 1 µg/ml, washing with TBST after 1 hour of incubation. Detection of bound IgG or HSA is achieved by the addition of streptavidin-HRP (Jackson Immunoresearch), followed by detection with POD substrate for chemiluminescence.

[000180] For purposes of the present invention, from 70 to 100% amino acid or nucleotide sequence identity (i.e., 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 or any range or value in that range) is determined using a suitable computer algorithm as is known in the art.

Tabela 2 - Sequências: SEQ ID n°: 1: MSGPVEVFITETPSQPNSHPIQWNAPQPSHISKYILRWRPKNSVGRW KEATIPGHLNSYTIKGLKPGVVYEGQLISIQQYGHQEVTRFDFTTTSTS GGHHHHHH SEQ ID n°: 2: MSGPVEVFITETPSQPNSHPIQWNAPQPSHISKYILRWRPKNSVGRW KEATIPGHLNSYTIKGLKPGVVYEGQLISIQQYGHQEVTRFDFTTTSTS GGHHHHHH SEQ ID n°: 3: MGAPDAPPDPTVDQVDDTSIVVRWSRPQAPITGYRIVYSPSVEGSST ELNLPETANSVTLSDLQPGVQYNITIYAVEENQESTPVVIQQETTGGH HHHHH SEQ ID n°: 4: MTVPSPRDLQFVEVTDVKVTIMWTPPESAVTGYRVDVIPVNLPGEHG QRLPISRNTFAEVTGLSPGVTYYFKVFAVSHGRESKPLTAQQTTGGH HHHHH SEQ ID n°: 5: MKLDAPTNLQFVNETDSTVLVRWTPPRAQITGYRLTVGLTRRGQPR QYNVGPSVSKYPLRNLQPASEYTVSLVAIKGNQESPKATGVFTTLGG HHHHHH SEQ ID n°: 6: MQPGSSIPPYNTEVTETTIVITWTPAPRIGFKLGVRPSQGGEAPREVT SDSGSIVVSGLTPGVEYVYTIQVLRDGQERDAPIVNKVVTGGHHHHH H SEQ ID n°: 7: MGLSPPTNLHLEANPDTGVLTVSWERSTTPDITGYRITTTPTNGQQG NSLEEVVHADQSSCTFDNLSPGLEYNVSVYTVKDDKESVPISDTIIPA GGHHHHHH SEQ ID n°: 8: MGVPPPTDLRFTNIGPDTMRVTWAPPPSIDLTNFLVRYSPVKNEEDV AELSISPSDNAVVLTNLLPGTEYVVSVSSVYEQHESTPLRGRQKTGG HHHHHH SEQ ID n°: 9: MLDSPTGIDFSDITANSFTVHWIAPRATITGYRIRHHPEHFSGRPRED RVPHSRNSITLTNLTPGTEYVVSIVALNGREESPLLIGQQSTGGHHHH HH SEQ ID n°: 10: MGVSDVPRDLEVVAATPTSLLISWDAPAVTVRYYRITYGETGGNSPV QEFTVPGSKSTATISGLKPGVDYTITVYAVTGRGDSPASSKPISINYRT GGHHHHHH SEQ ID n°: 11: MGEIDKPSQMQVTDVQDNSISVKWLPSSSPVTGYRVTTTPKNGPGP TKTKTAGPDQTEMTIEGLQPTVEYVVSVYAQNPSGESQPLVQTAVTG GHHHHHH SEQ ID n°: 12: MTIPAPTDLKFTQVTPTSLSAQWTPPNVQLTGYRVRVTPKEKTGPMK EINLAPDSSSVVVSGLMVATKYEVSVYALKDTLTSRPAQGVVTTLGG HHHHHH SEQ ID n°: 13: MENVSPPRRARVTDATETTITISWRTKTETITGFQVDAVPANGQTPIQ RTIKPDVRSYTITGLQPGTDYKIYLYTLNDNARSSPVVIDASTGGHHH HHH SEQ ID n°: 14: MAIDAPSNLRFLATTPNSLLVSWQPPRARITGYIIKYEKPGSPPREVVP RPRPGVTEATITGLEPGTEYTIYVIALKNNQKSEPLIGRKKTGGHHHH HH SEQ ID n°: 15: MGHRPRPYPPNVGQEALSQTTISWAPFQDTSEYIISCHPVGTDEEPL QFRVPGTSTSATLTGLTRGATYNIIVEALKDQQRHKVREEVVTVGNS GGHHHHHH SEQ ID n°: 16: MPAPTDLRFTNETPSSLLISWTPPRVQITGYIIRYGPVGSDGRVKEFT VPPSVSSATITGLKPGTEYTISVIALKDNQESEPLRGRVTTGGHHHHH H SEQ ID n°: 17: atgccggcgccgaccgatctgcgctttaccaacgaaaccccgagcagcctgctgattagctgga ccccgccgcgcgtgcagattaccggctatattattcgctatggcccggtgggcagcgatggccgc gtgaaagaatttaccgtgccgccgagcgtgagcagcgcgaccattaccggcctgaaaccgggc accgaatataccattagcgtgattgcgctgaaagataaccaggaaaTabela 3 - Laços de fibcon

[000181] It will be clear that the invention can be put into practice in another way than that particularly described in the above-mentioned description and examples. Numerous modifications and variations of the present invention are possible in light of the above teachings and are therefore within the scope of the appended claims. Table 1 Melting temperatures of the FN3 domains, as determined by differential scanning calorimetry.

Table 2 - Sequence: SEQ ID NO: 1: MSGPVEVFITETPSQPNSHPIQWNAPQPSHISKYILRWRPKNSVGRW KEATIPGHLNSYTIKGLKPGVVYEGQLISIQQYGHQEVTRFDFTTTSTS GGHHHHHH SEQ ID NO: 2: MSGPVEVFITETPSQPNSHPIQWNAPQPSHISKYILRWRPKNSVGRW KEATIPGHLNSYTIKGLKPGVVYEGQLISIQQYGHQEVTRFDFTTTSTS GGHHHHHH SEQ ID NO: 3: MGAPDAPPDPTVDQVDDTSIVVRWSRPQAPITGYRIVYSPSVEGSST ELNLPETANSVTLSDLQPGVQYNITIYAVEENQESTPVVIQQETTGGH HHHHH SEQ ID NO: 4: MTVPSPRDLQFVEVTDVKVTIMWTPPESAVTGYRVDVIPVNLPGEHG QRLPISRNTFAEVTGLSPGVTYYFKVFAVSHGRESKPLTAQQTTGGH HHHHH SEQ ID NO: 5: MKLDAPTNLQFVNETDSTVLVRWTPPRAQITGYRLTVGLTRRGQPR QYNVGPSVSKYPLRNLQPASEYTVSLVAIKGNQESPKATGVFTTLGG HHHHHH SEQ ID NO: 6: H MQPGSSIPPYNTEVTETTIVITWTPAPRIGFKLGVRPSQGGEAPREVT SDSGSIVVSGLTPGVEYVYTIQVLRDGQERDAPIVNKVVTGGHHHHH SEQ ID NO: 7: MGLSPPTNLHLEANPDTGVLTVSWERSTTPDITGYRITTTPTNGQQG NSLEEVVHADQSSCTFDNLSPGLEYNVSVYTVKDDKESVPISDTIIPA GGHHHHHH SEQ ID NO: 8: MGVPPPTDLRFTNIGPDTMRVTWAPPPSIDLTNFLVRYSPVKNEEDV AELSISPSDNAVVLTNLLPGTEYVVSVSSVYEQHESTPLRGRQKTGG HHHHHH SEQ ID NO: 9: MLDSPTGIDFSDITANSFTVHW IAPRATITGYRIRHHPEHFSGRPRED RVPHSRNSITLTNLTPGTEYVVSIVALNGREESPLLIGQQSTGGHHHH HH SEQ ID No.: 10: MGVSDVPRDLEVVAATPTSLLISWDAPAVTVRYYRITYGETGGNSPV QEFTVPGSKSTATISGLKPGVDYTITVYAVTGRGDSPASSKPISINYRT GGHHHHHH SEQ ID NO: 11: MGEIDKPSQMQVTDVQDNSISVKWLPSSSPVTGYRVTTTPKNGPGP TKTKTAGPDQTEMTIEGLQPTVEYVVSVYAQNPSGESQPLVQTAVTG GHHHHHH SEQ ID NO: 12: MTIPAPTDLKFTQVTPTSLSAQWTPPNVQLTGYRVRVTPKEKTGPMK EINLAPDSSSVVVSGLMVATKYEVSVYALKDTLTSRPAQGVVTTLGG HHHHHH SEQ ID NO: 13: MENVSPPRRARVTDATETTITISWRTKTETITGFQVDAVPANGQTPIQ RTIKPDVRSYTITGLQPGTDYKIYLYTLNDNARSSPVVIDASTGGHHH HHH SEQ ID NO: 14: MAIDAPSNLRFLATTPNSLLVSWQPPRARITGYIIKYEKPGSPPREVVP RPRPGVTEATITGLEPGTEYTIYVIALKNNQKSEPLIGRKKTGGHHHH HH SEQ ID NO: 15: MGHRPRPYPPNVGQEALSQTTISWAPFQDTSEYIISCHPVGTDEEPL QFRVPGTSTSATLTGLTRGATYNIIVEALKDQQRHKVREEVVTVGNS GGHHHHHH SEQ ID NO: 16: MPAPTDLRFTNETPSSLLISWTPPRVQITGYIIRYGPVGSDGRVKEFT H VPPSVSSATITGLKPGTEYTISVIALKDNQESEPLRGRVTTGGHHHHH SEQ ID NO: 17: atgccggcgccgaccgatctgcgctttaccaacgaaaccccgagcagcctgctgattagctgga ccccgccgcgcgtg cagattaccggctatattattcgctatggcccggtgggcagcgatggccgc gtgaaagaatttaccgtgccgccgagcgtgagcagcgcgaccattaccggcctgaaaccgggc accgaatataccattagcgtgattgcgctgaaagataaccaggaaaTable 3 - Fibcon loops

Claims (9)

1. Isolated protein framework, characterized in that it comprises a fibronectin type III (FN3) domain, which comprises 7 strands and 6 loops between strands and is defined by the amino acid sequence of SEQ ID NO: 16. 2. Protein framework, according to claim 1, characterized in that the loops form sites to bind targets. 3. Method for constructing a library of a protein scaffold as defined in claim 1 or 2, said method characterized in that it comprises the steps of: obtaining a polypeptide having the amino acid sequence of SEQ ID NO: 16, and introducing diversity into copies of the polypeptide having the amino acid sequence of SEQ ID NO: 16, to form the protein scaffold library, optionally wherein introducing the diversity step comprises mutating at least one loop region selected from the group consisting of residues 13 to 16, 22 to 28, 38 to 43, 51 to 54, 60 to 64, and 75 to 81 of SEQ ID NO:16 4. An isolated nucleic acid molecule, characterized in that it comprises the nucleotide sequence shown in SEQ ID NO: 17. 5. Isolated nucleic acid vector, characterized in that it comprises the isolated nucleic acid molecule as defined in claim 4. 6. Bacterial or fungal host cell, characterized in that it comprises the isolated nucleic acid molecule, as defined in claim 4, wherein said host cell is at least one selected from E. coli BL21Star(DE3), another E. coli cell and yeast. 7. A composition, characterized in that it comprises a protein scaffold as defined in claim 1 or 2, and at least one pharmaceutically acceptable carrier or diluent, optionally further comprising at least one compound or polypeptide selected from a reporter or a detectable label, a TNF antagonist, an anti-infective drug, a cardiovascular (CV) drug, a central nervous system (CNS) drug, an autonomic nervous system (ANS) drug, a respiratory tract, a drug for the gastrointestinal (GI) tract, a hormonal drug, a drug for fluid or electrolyte balance, a hematologic drug, an antineoplastic, a drug for immunomodulation, an ophthalmic, optical or nasal drug, a drug of use topical, a nutritional drug, a cytokine and a cytokine antagonist. 8. Medical device, characterized in that it comprises a protein scaffold as defined in claim 1 or 2, wherein said device is suitable for contacting or administering said protein scaffold by at least one mode selected from parenteral, subcutaneous, intramuscular, intravenous, intra-articulatory, intrabronchial, intra-abdominal, intracapsular, intracartilaginous, intracavitary, intraceliac, intracerebellar, intracerebroventricular, intracolic, intracervical, intragastric, intrahepatic, intramyocardial, intraosseous, intrapelvic, intraperi- cardiac, intraperitoneal, intrapleural, intraprostatic, intrapulmonary, intrarectal, intrarenal, intraretinal, intraspinal, intrasynovial, intrathoracic, intrauterine, intravesicular, intralesional, bolus, vaginal, rectal, buccal, sublingual, intranasal and transdermal. An article of manufacture for human pharmaceutical or diagnostic use, comprising packaging material and a container comprising a solution or a lyophilized form of a protein scaffold as defined in claim 1 or 2, wherein said container is a component of a parenteral, subcutaneous, intramuscular, intravenous, intra-articulatory, intrabronchial, intra-abdominal, intracapsular, intracartilaginous, intracavitary, intraceliac, intracerebellar, intracerebroventricular, intracolic, intracervical, intragastric, intrahepatic, delivery device or system. intramyocardial, intraosseous, intrapelvic, intrapericardial, intraperitoneal, intrapleural, intraprostatic, intrapulmonary, intrarectal, intrarenal, intraretinal, intraspinal, intrasynovial, intrathoracic, intrauterine, intravesicular, intralesional, bolus, vaginal, rectal, buccal, sublingual, intranasal, or transdermal.

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